Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of metabolically labelled RNA by 4-thiouracil from mouse tissues

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 1500

ORGANISM(S): Mus musculus

SUBMITTER: Wayo Matsushima

PROVIDER: E-MTAB-6353 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

TU-tagging: cell type specific RNA isolation from intact complex tissues

Project description:We show that the combination of spatially restricted uracil phosphoribosyltransferase (UPRT) expression with 4-thiouracil (4TU) delivery can be used to label and purify cell type specific RNA from intact complex tissues. This method is useful for isolating RNA from cell types that are difficult to isolate by dissection or dissociation methods and should work in any organism where UPRT can be spatially expressed, including mammals and other vertebrates. To confirm that thio-labeled RNA was from UPRT-expressing cells and demonstrate the utility of TU-tagging for cell type-specific RNA isolation, we purified TU-tagged and untagged RNA and compared them using microarrays. We chose to isolate RNA from larval glia, which are present in low number, are highly dispersed, and have a complex cell morphology, making them one of the most difficult cell types to isolate by dissection or dissociation methods. We used reversed polarity (repo)-GAL4 to drive expression of UAS-UPRT specifically in glial cells of the larval brain. We purified TU-tagged and untagged RNA from 72-96h larval brains, and hybridized them to custom Agilent microarrays. We performed two biological replicate experiments.

2010-06-19 | E-GEOD-15445 | biostudies-arrayexpress

TU-tagging: cell type specific RNA isolation from intact complex tissues

2009-04-24 | GSE15445 | GEO

Transcription profiling of UPRT transgenic and wild type control cells of both HeLa and U373MG tissue culture lines grown in the presence of 2mM 2,4-dithiouracil for either 6 hours (HeLa) or 8 hours (U373MG) and total RNA, not thiouracil-purified, from both transgenic and wild type samples

Project description:UPRT Transgenic and wildtype control cells of both HeLa and U373MG tissue culture lines were grown in the presence of 2mM 2,4-dithiouracil for either 6 hours (HeLa) or 8 hours (U373MG) and total RNA, not thiouracil-purified, from both transgenic and wildtype samples was compared on microarrays.

2005-07-07 | E-SMDB-3404 | biostudies-arrayexpress

Transcription profiling of liver from hypothyroid mice pups produced from dams given 6-propyl-2-thiouracil (PTU) in their drinking water

Project description:Pregnant dams were treated with 0.1% or 0.04% 6-propyl-2-thiouracil (PTU) in drinking water continuously from day 13 post conception until weaning to produce hypothyroid pups. livers were collected from vehicle and 0.1% PTU treated pups at post-natal day (PND) 15 and mRNA from these was subjected to microarray analysis using Agilent high-density oligonucleotide chips.

2007-05-03 | E-MEXP-1091 | biostudies-arrayexpress

Cell-specific analysis of mRNA synthesis and decay

Project description:This SuperSeries is composed of the following subset Series: GSE2946: Synthesis vs. Abundance, Bradyzoite Development GSE2947: Thiouracil Pulse-chase, Tachyzoites and Bradyzoites mRNA stability data GSE2948: UPRT Transgenic cells, Human Arrays Abstract: Standard microarrays measure mRNA abundance, not mRNA synthesis, and therefore cannot identify the mechanisms that regulate gene expression. We have developed a method to overcome this limitation by using the salvage enzyme uracil phosphoribosyltransferase (UPRT) from the protozoan Toxoplasma gondii. T. gondii UPRT has been well characterized because of its application in monitoring parasite growth: mammals lack this enzyme activity and thus only the parasite incorporates (3)H-uracil into its nucleic acids. In this study we used RNA labeling by UPRT to determine the roles of mRNA synthesis and decay in the control of gene expression during T. gondii asexual development. We also used this approach to specifically label parasite RNA during a mouse infection and to incorporate thio-substituted uridines into the RNA of human cells engineered to express T. gondii UPRT, indicating that engineered UPRT expression will allow cell-specific analysis of gene expression in organisms other than T. gondii. Refer to individual Series

2006-03-07 | E-GEOD-4401 | biostudies-arrayexpress

uprt overexpression - Transcriptomic analysis of overexpression of the URPT gene

Project description:adt10-02_35suprt - uprt overexpression. Transcriptomic analysis of the overexpression of UPTR. 8 dye-swaps. Normal vs. transgenic comparison.

2011-02-01 | E-GEOD-26847 | biostudies-arrayexpress

UPRT Transgenic cells, Human Arrays

2005-07-16 | E-GEOD-2948 | biostudies-arrayexpress

UPRT Transgenic cells, Human Arrays

2005-07-16 | GSE2948 | GEO

Transcription profiling of Toxoplasma gondii thiouracil pulse-chase, tachyzoites and bradyzoites mRNA stability data

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

plant rabt nÂ°1-Plant RABT nÂ°1

Project description:adt12-01_uprt - plant rabt nÂ°1 - Impact of RNA labeling by Plant RABT on plant transcriptome - Determine the incidence of RNA marking by the RABT method Plantation on the plants transcriptome. In several studies Clearly et al. have described a method referred as "4TU tagging" which can be use to study mRNA synthesis and decay either in a mixed population of cells or in a specific cell type (Cleary, Meiering et al. 2005, Zeiner, Cleary et al. 2008, Miller, Robinson et al. 2009, Rabani et al., 2011). Through the specific cell type expression in drosophila and mammalian cells of theToxoplasma gondii uracil PhosphoribosylTransferase activity and the metabolization of the uracil analog 4-thiouracil (4 TU), mRNA were selectively tagged, purified and used in microarray based analysis. 6 dye-swap - treated vs untreated comparison

2014-09-10 | E-GEOD-60532 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data