Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MAPCap enables high-resolution detection and differential expression analysis of transcription start sites

ABSTRACT: MAPCap enables high-resolution detection and differential expression analysis of transcription start sites

PROVIDER: PRJNA517665 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

MAPCap enables high-resolution detection and differential expression analysis of transcription start sites

Project description:Promoter architecture, shape and usage play an important role in the regulation of eukaryotic gene expression. Several promoter profiling techniques have been developed to detect transcription start sites and alternative promoter usage between tissues or during development. However promoter profiling has not been utilized in studies that demand quantification of expression changes between developmental stages, tissues and conditions. In this study, we combine promoter profiling and differential expression analysis in a single setup, using a fast and simple protocol, MAPCap (Multiplexed Affinity Purification of Capped RNA) along with a new software “icetea” (https://bioconductor.org/packages/icetea). The use of random molecular barcodes and spike-ins in MAPCap enables accurate quantification of expression from promoters. We detected sex-specific promoter usage in the brains of Drosophila melanogaster larvae. Comparison of male and female mutant flies of the male-less helicase (MLE), a protein known to be essential for the dosage compensation of the male X-chromosome, indicated that the sensitivity of promoters to dosage compensation depends on their genomic location. Our results expand the scope of promoter profiling methods to differential expression analysis and provide quantitative insights into promoter usage during dosage compensation.

2019-06-04 | GSE125831 | GEO

MAPCap allows high-resolution detection and differential expression analysis of transcription start sites.

Project description: Not available

| S-EPMC6667505 | biostudies-literature

Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection

Project description:This SuperSeries is composed of the following subset Series: GSE15746: Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 1 GSE15747: Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 2 Refer to individual Series

2010-05-19 | E-GEOD-15801 | biostudies-arrayexpress

Detection of cryptic start codons in set2D by 5PSeq

Project description:Detection of cryptic start codons in set2D by 5PSeq

| PRJNA486741 | ENA

BABEL enables cross-modality translation between multi-omic profiles at single-cell resolution

Project description:BABEL enables cross-modality translation between multi-omic profiles at single-cell resolution

2021-02-16 | GSE166797 | GEO

Discovery of diverse DNA cytosine deaminases enables a single-enzyme method for base resolution methylation detection

Project description:Cytosine deaminases have important uses in the detection of epigenetic modifications and in genome editing. However, the range of applications of deaminases is limited by their substrate preference. To expand the toolkit of deaminases, we developed an in-vitro approach that bypasses a major hurdle with their severe toxicity in expression hosts. We screened 175 putative cytosine deaminases, primarily from bacteria, and found enzymes with strong activity on double- and single-stranded DNA in various sequence contexts, including some without any sequence constraints. We also found enzymes that do not deaminate modified cytosines. The remarkable diversity of cytosine deaminases opens new avenues for biotechnological and medical applications. As a demonstration, we developed a single-enzyme methylation sequencing (SEM-seq) method for 5-methylcytosine detection using a novel non-specific, modification-sensitive double-stranded DNA deaminase, MsddA. SEM-seq generated accurate base-resolution maps of 5-methylcytosine in human genome samples including cell free DNA and samples of 10 pg DNA, equivalent to single cell input. This simple and efficient protocol has the potential to allow high-throughput epigenome profiling of scarce biological material.

2023-10-05 | GSE233932 | GEO

Multi-functional barcoding enables high resolution study of clonal dynamics

Project description:Multi-functional barcoding enables high resolution study of clonal dynamics

| PRJNA635808 | ENA

DARESOME enables concurrent profiling of multiple DNA modifications in single cells and multi-omics detection of cancer signatures in cell-free DNA

Project description:DARESOME enables concurrent profiling of multiple DNA modifications in single cells and multi-omics detection of cancer signatures in cell-free DNA

2023-08-04 | GSE207918 | GEO

SUGAR-Seq enables simultaneous detection of glycans, epitopes and the transcriptome in single cells [ATAC-seq]

Project description:Multi-modal single cell RNA sequencing enables the precise mapping of transcriptional and phenotypic features of cellular differentiation states, but does not allow for simultaneous integration of critical post-translational modification data. Here, we describe SUrface-protein Glycan And RNA-seq (SUGAR-seq); a method that enables detection and analysis of N-linked glycosylation, extracellular epitopes and the transcriptome at the single cell level. Integrated SUGAR-seq and glycoproteome analysis identified tumor infiltrating T cells with unique surface glycan properties that report their epigenetic and functional state.

2021-02-22 | GSE166324 | GEO

SUGAR-Seq enables simultaneous detection of glycans, epitopes and the transcriptome in single cells [TIL scRNA-seq]

2021-02-22 | GSE166326 | 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