Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin-dependent regulation of the RNA polymerases II and III activity throughout the transcription cycle

ABSTRACT: We have developed a new genome-wide protocol for nascent transcription analysis at high resolution in the yeast Saccharomyces cerevisiae. This protocol is based in run-on labeling of nascent RNA with a biotinylated precursor. We call it BioGRO for biotin-based genomic run-on.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE58859 | GEO | 2014/12/01

SECONDARY ACCESSION(S): PRJNA253732

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

PROseq (Precision Run-On sequencing) to capture nascent RNA of wild type and mutant mouse embryonic stem cells

Project description:Precision Run-On Sequencing (PROseq) data for wild type (WT) and mutant mouse embryonic stem cells from Kreibich et al., 2022. PROseq data was obtained by permeabilizing the cells, performing a 2 biotin run-on reaction using biotin-11-UTP and biotin-11-CTP and subsequent enrichments steps for biotinylated RNA during the library preparation. This results in the enrichment of nascent transcripts, including enhancer RNA. Data in this experiment comprises PROseq data obtained from WT mouse embryonic stem cells (ES) and DNA methylation mutants (DNMT TKO ES and TET TKO ES). Comparing the PROseq data obtained from these different cell lines enables the detection of changes in the activity of cis-regulatory elements upon changes in DNA methylation.

2023-02-06 | E-MTAB-12601 | biostudies-arrayexpress

Total and Nascent Transcriptome of Xenopus laevis Embryos at 5-9 hpf (stage 7-9)

Project description:To characterize the nascent transcriptome during zygotic genome activation (ZGA) of Xenopus laevis embryos, we microinjected 5-ethynyl uridine (EU) into 1-cell stage embryos and isolated total RNAs from whole embryos at 5, 6, 7, 8 and 9 hours post-fertilization (hpf) at room temperature, respectively, covering the stages of pre-ZGA to widespread ZGA (stage 7-9). To purify nascent transcripts, total RNAs were biotinylated using disulfide biotin azide via click reaction and biotinylated nascent transcripts were purified using streptavidin beads. Libraries were constructed from using the total RNA ('All'), nascent transcripts ('Bead') and the flowthrough after purification of nascent transcripts ('FL'), respectively. To categorize maternal-zygotic (MZ) genes and zygotic-only (Z) genes, total RNAs from eggs were isolated for constructing libraries. All libraries were sequenced on illumina NextSeq 500.

2022-08-22 | GSE201835 | GEO

Quantification of transcriptional changes during in vivo mouse erythropoiesis by nascent RNA-sequencing

Project description:We isolated erythroid progenitor cells at various stages of differentiation from mouse fetal liver using flow cytometry. We metabolically labelled RNA from purified progenitor populations with 4-thiouridine (4sU) for 45 minutes in ex vivo culture, then extracted cellular RNA. Nascent RNA was biotinylated by reaction of the incorporated thiol groups with MTS-Biotin, then purified using streptavidin nanobeads and sequenced.

2020-11-02 | GSE159229 | GEO

Nascent Transcriptome of AP and VP from Xenopus laevis Embryos at 5-9 hpf (stage 7-9)

Project description:To characterize the spatial patterns of zygtoic transcription during zygotic genome activation (ZGA) of Xenopus laevis embryos, we microinjected 5-ethynyl uridine (EU) into 1-cell stage embryos and isolated total RNAs from whole embryos at 5, 6, 7, 8 and 9 hours post-fertilization (hpf) at room temperature, respectively, covering the stages of pre-ZGA to widespread ZGA (stage 7-9). The animal pole (AP, ~ 1/3 at the top region of embryo) and the vegetal pole (VP,~ 1/3 at the bottom region of embryo) regions were dissected and used for total RNA isolation. To purify nascent transcripts, total RNAs were biotinylated using disulfide biotin azide via click reaction and biotinylated nascent transcripts were purified using streptavidin beads. Libraries were constructed from using the nascent transcripts. All libraries were sequenced on illumina NextSeq 500.

2022-08-22 | GSE201833 | GEO

Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle.

Project description: Not available

| S-EPMC4333398 | biostudies-literature

PRO-IP-seq: Pol II CTD code at nt-resolution in human K562 cells

Project description:Active sites of transcription were labelled with biotinylated nucleotide during a run-on reacation, where after an immunoprecipitation with antibodies that target Pol II CTD was conducted. This PRO-IP-seq protocol was conducted in human K562 erythroleukemia cells. The K562 cells were either untreated (NHS) or treated with 30 minutes of heat shock at 42°C (HS).

2023-02-24 | GSE200269 | GEO

OXIPEP: mass spectrometry strategy to characterize protein carbonylation.

Project description:Here we describe a peptide-centric approach (OXIPEP), where carbonylated residues within proteins are derivatized with biotin-hydrazide, enriched and identified by mass spectrometry. The strength of the method lies in an improved protocol for elution of biotinylated peptides from monomeric avidin resin using hot water (95C) and increased sensitivity achieved by reduction of sample losses during sample preparation and chromatographic steps. For the first time advanced bioinformatics analysis utilising diagnostic biotin fragment ions is used to facilitate semi-automatic in silico evaluation of biotin labelling and to increase the reliability of carbonyl peptide identification.

2018-10-18 | PXD002966 | Pride

Rapid and scalable profiling of nascent RNA with fastGRO

Project description:We developed a new method to profile nascent RNA in mammalian cells. The new methodology is based on the incorporation of thio-UTP, an analog of UTP, during in vitro RNA Polymerase run-on.

2020-01-17 | GSE143844 | GEO

Off the shelf proximity biotinylation using ProtA-TurboID

Project description:Proximity biotinylation is a commonly used method to identify the in vivo proximal proteome for proteins of interest. This technology typically relies on fusing a bait protein to a biotin ligase using overexpression or CRISPR-based tagging, thus prohibiting such assays in (primary) cell types that are difficult to transfect. We recently developed an ‘off the shelf’ proximity biotinylation method, which makes use of a recombinant enzyme consisting of the biotin ligase TurboID fused to the antibody-recognizing moiety Protein A. In this method, a bait specific antibody and the ProteinA-Turbo enzyme are consecutively added to permeabilized fixed or unfixed cells. Following incubation, during which ProteinA-Turbo-antibody-antigen complexes are formed, unbound molecules are washed away, after which bait-proximal biotinylation is triggered by the addition of exogenous biotin. Finally, biotinylated proteins are enriched from crude lysates using streptavidin beads followed by mass spectrometry-based protein identification. Here, we present a detailed protocol for this method

2022-10-17 | PXD030963 | Pride

HSP70 binds RNA and regulates transcription by RNA Polymerase III [RNA-seq]

Project description:We examined the RNA binding ability of the 70-kDa heat shock protein (HSP70) family member HSPA1A and identified the RNA species bound to HSP70 in vivo. We used a UV-crosslinkiung and immunoprecipitation based approach named FLASH-seq (Aktaş et al., 2017) using 3xFLAG-Histidine-Biotin tagged ectopically expressed protein in HEK293T cells.

2024-01-17 | GSE191244 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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