Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A framework to validate fluorescently labeled DNA-binding proteins for single-molecule experiments

ABSTRACT: A framework to validate fluorescently labeled DNA-binding proteins for single-molecule experiments

PROVIDER: PRJNA877201 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR21439981_1.fastq.gz	Fastqsanger.gz
	SRR21439981_2.fastq.gz	Fastqsanger.gz
	SRR21439982_1.fastq.gz	Fastqsanger.gz
	SRR21439982_2.fastq.gz	Fastqsanger.gz
	SRR21439983_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

A framework to validate fluorescently labeled DNA-binding proteins for single-molecule experiments

Project description:Due to the enhanced labeling capability of maleimide-based fluorescent probes, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. In this study, we employed in vitro single-molecule DNA flow-stretching assay as a sensitive way to assess the impact of the KCK-tag on the property of DNA-binding proteins. Using Bacillus subtilis ParB as an example, we show that, although no noticeable changes were detected by in vivo fluorescence imaging and chromatin immunoprecipitation (ChIP) assays, the KCK-tag substantially altered ParB’s DNA compaction rates, its response to nucleotide binding and to the presence of the specific sequence (parS) on the DNA. While it is typically assumed that short peptide tags minimally perturb protein function, our results urge researchers to carefully validate the use of tags for protein labeling. Our comprehensive analysis can be expanded and used as a guide to assess the impacts of other tags on DNA-binding proteins in single-molecule assays.

2023-09-30 | GSE212751 | GEO

Transcription profiling of E12.5 mouse whole embryos and placentas pooled within 3 litters to validate a new array

Project description:E12.5 mouse whole embryos and placentas were pooled within 3 litters and total RNA was extracted. Fluorescently-labeled, linearly-amplified cRNA targets were prepared from the RNA samples and compared on a novel microarray design to validate the system. A "dye-swapped" experimental design was used to assess the accuracy and precision of the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 22,000 DNA features, and was designed to detect transcripts from the entire NIA cDNA clone collection.

2005-01-01 | E-MNIA-69 | biostudies-arrayexpress

BrU-labeled nascent RNA sequencing and m6A-IP from BrU-labeled nascent RNA

Project description:BrU-labeled nascent RNA sequencing and m6A-IP from BrU-labeled nascent RNA

| PRJNA326350 | ENA

A method to investigate muscle target-specific transcriptional signatures of single motor neurons

Project description:To investigate target-specific transcriptional signatures of single motor neurons, here we combine ex-ovo retrograde axonal labelling in mid-gestation chicken embryos with manual isolation of individual fluorescent cells and Smart-seq2 single-cell RNA-sequencing. We validate our method by injecting the EMR and FDQ wing muscles and harvest a total of 50 fluorescently labeled cells, in which we detect upto 10000 transcribed genes. Additionally, we present visual cues and cDNA metrics predictive of sequencing success.

2022-07-29 | GSE203595 | GEO

4sU metabolic labeled transcripts in mESCs

Project description:4sU metabolic labeled transcripts in mESCs

| PRJNA438673 | ENA

Extracellular vesicle labeled Granulocyte macrophage progenitors

Project description:Extracellular vesicle labeled Granulocyte macrophage progenitors

| PRJNA525660 | ENA

Using shRNA experiments to validate gene regulatory networks.

Project description:Quantitative validation of gene regulatory networks (GRNs) inferred from observational expression data is a difficult task usually involving time intensive and costly laboratory experiments. We were able to show that gene knock-down experiments can be used to quantitatively assess the quality of large-scale GRNs via a purely data-driven approach (Olsen et al. 2014). Our new validation framework also enables the statistical comparison of multiple network inference techniques, which was a long-standing challenge in the field. In this Data in Brief we detail the contents and quality controls for the gene expression data (available from NCBI Gene Expression Omnibus repository with accession number GSE53091) associated with our study published in Genomics (Olsen et al. 2014). We also provide R code to access the data and reproduce the analysis presented in this article.

| S-EPMC4535466 | biostudies-literature

Manipulation experiments metagenomes

Project description:Manipulation experiments metagenomes

| PRJEB64576 | ENA

[KIL-d] experiments

Project description:[KIL-d] experiments

| PRJEB11279 | ENA

Identification and quantification of within-burst dynamics in singly labeled single-molecule fluorescence lifetime experiments.

Project description:Single-molecule spectroscopy has revolutionized molecular biophysics and provided means to probe how structural moieties within biomolecules spatially reorganize at different timescales. There are several single-molecule methodologies that probe local structural dynamics in the vicinity of a single dye-labeled residue, which rely on fluorescence lifetimes as readout. Nevertheless, an analytical framework to quantify dynamics in such single-molecule single dye fluorescence bursts, at timescales of microseconds to milliseconds, has not yet been demonstrated. Here, we suggest an analytical framework for identifying and quantifying within-burst lifetime-based dynamics, such as conformational dynamics recorded in single-molecule photo-isomerization-related fluorescence enhancement. After testing the capabilities of the analysis on simulations, we proceed to exhibit within-burst millisecond local structural dynamics in the unbound α-synuclein monomer. The analytical framework provided in this work paves the way for extracting a full picture of the energy landscape for the coordinate probed by fluorescence lifetime-based single-molecule measurements.

| S-EPMC9534301 | biostudies-literature

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