Metabolic labeling of Hek293 cells using 4-thiouracil
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ABSTRACT:
PROVIDER: PRJNA476121 | ENA |
REPOSITORIES: ENA
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Project description:Hek293 cells were metabolically labelled using 4-thiouracil as described in (Schwalb et al, Science. 2016 Jun 3;352(6290):1225-8) but without fragmentation, and then bulk RNA was prepared for sequencing using the STRT method (Islam et al, Genome Res. 2011 Jul;21(7):1160-7). Samples were incubated in duplicate for 5, 15 and 30 minutes and included an unlabeled control representing the steady-state expression state.
2018-08-09 | GSE115813 | GEO
Project description:We measure the stability of mRNAs in rapidly dividing yeast by metabolic labeling with thiouracil and determine the effects on mRNA stability in the presence of various inhibitors of translation elongation and initiation.
2018-09-07 | GSE119560 | GEO
Project description:Pulse chase measurements using thiouracil (DTU) labeling via UPRT and chasing with uracil Data from tachyzoites is labeled "DTU Pulse Chase". Two independent pulse chase experiments were performed in tachyzoites, pulse chase 1 and 2. Duplicate arrays at each timepoint were performed for pulse chase 2 (2 a and b). Data from bradyzoites are labeled "DTU Bradyzoite Pulse Chase". Two independent pulse chase experiments were performed in bradyzoites and a single set of arrays were performed for each experiment. Just one chase timepoint was used in the bradyzoite experiments, the 2 hour chase. An RNA stablity experiment design type examines stability and/or decay of RNA transcripts. Keywords: RNA_stability_design
2005-07-16 | GSE2947 | GEO
Project description:Pulse chase measurements using thiouracil (DTU) labeling via UPRT and chasing with uracil Data from tachyzoites is labeled "DTU Pulse Chase". Two independent pulse chase experiments were performed in tachyzoites, pulse chase 1 and 2. Duplicate arrays at each timepoint were performed for pulse chase 2 (2 a and b). Data from bradyzoites are labeled "DTU Bradyzoite Pulse Chase". Two independent pulse chase experiments were performed in bradyzoites and a single set of arrays were performed for each experiment. Just one chase timepoint was used in the bradyzoite experiments, the 2 hour chase. An RNA stablity experiment design type examines stability and/or decay of RNA transcripts. User Defined
2005-07-16 | E-GEOD-2947 | biostudies-arrayexpress
Project description:Pulse chase measurements using thiouracil (DTU) labeling via UPRT and chasing with uracil Data from tachyzoites is labeled "DTU Pulse Chase". Two independent pulse chase experiments were performed in tachyzoites, pulse chase 1 and 2. Duplicate arrays at each timepoint were performed for pulse chase 2 (2 a and b). Data from bradyzoites are labeled "DTU Bradyzoite Pulse Chase". Two independent pulse chase experiments were performed in bradyzoites and a single set of arrays were performed for each experiment. Just one chase timepoint was used in the bradyzoite experiments, the 2 hour chase.
2005-07-07 | E-SMDB-2949 | biostudies-arrayexpress
Project description:An Optimized Chemical-Genetic Method for Cell-Specific Metabolic Labeling of RNA
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Project description:To identify cell type-specific RNA without cell sorting, mice expressing UPRT in a specific cell type were exposed to 4-thiouracil to label RNA only in the UPRT-expressing cells. Total RNA was extracted from tissues and treated with iodoacetamide followed by RNA-seq library preparation. The reads generated from 4-thiouracil-containing transcripts should contain T to C mismatches as a result of 4-thiouracil incorporations and thus can be identified as the transcripts generated in the UPRT-expressing cells.
2018-07-09 | E-MTAB-6353 | biostudies-arrayexpress
Project description:Histone acetylation is an important, reversible posttranslational protein modification and hallmark of epigenetic regulation. However, little is known about the dynamics of reversible hisotne acetylation, due to the lack of analytical methods that can capture site-specific acetylation and deacetylation reactions. We present a new approach that combines metabolic and chemical labeling (CoMetChem) using uniformly 13C-labeled glucose and stable isotope labeled acetic anhydride, which allows to quantify site-specific lysine acetylation dynamics in tryptic peptides using high-resolution mass spectrometry.
2021-11-02 | PXD027338 | Pride
Project description:Dinoflagellates possess many physiological processes that appear to be under post-transcriptional control. However, the extent to which their genes are regulated post-transcriptionally remains unresolved. To gain insight into role of de novo transcription in dinoflagellates, we biosynthetically labeled RNA with 4-thiouracil to isolate newly transcribed RNA in Karenia brevis. These isolated fractions were then used for analysis of global de novo transcription by hybridization to a K. brevis microarray. As previous microarray studies indicated that transcripts for pentatricopeptide repeat (PPR) proteins rapidly increased in response to nutrient addition, we queried the newly synthesized RNA pools at 1 and 4 h following nitrate addition to N-depleted cultures. Transcriptome-wide there was little evidence of changes in the rate of de novo transcription during the first 4 h, relative to that in N-depleted cells, and no evidence for increased PPR protein transcription. These results lend support to the growing consensus of post-transcriptional control of gene expression in dinoflagellates.M-bM-^@M-^C Cultures were acclimated to 10 M-BM-5M nitrate for a minimum of two months during which time cultures were transferred weekly in log phase. For addition experiments, nutrient replete and N-limited 1 L cultures were grown to stationary phase (Day 9). Using sodium nitrate, 155 M-BM-5M NO3 was added to stationary phase cultures. Cultures were exposed to 0.2 mM 4-thiouracil for 1 h to biosynthetically label newly transcribed RNA during the first hour post-N-addition (n=3) or during the fourth hour post-N-addition (n=3). N-limited cultures (n=3) were also exposed to 0.2 mM 4-thiouracil for 1 h to biosynthetically label newly transcribed RNA. Cultures were harvested after 1 h exposure to 4-thiouracil and total RNA extracted. Following extraction, RNA was biotinylated to allow for purification of the thiolated newly synthesized RNA from the total RNA pool using streptavidin coated magnetic beads. The newly transcribed RNA from each culture was independently labeled and hybridized to microarrys in a one color format. Based on the appearance of bioanlayzer profiles newly synthesized RNA was treated as mRNA in the labeling protocol.
2013-08-01 | E-GEOD-46175 | biostudies-arrayexpress
Project description:Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome
| PRJNA485744 | ENA