Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Long-TUC-seq is a robust method for quantification of metabolically labeled full-length isoforms

ABSTRACT: Long-TUC-seq is a robust method for quantification of metabolically labeled full-length isoforms

PROVIDER: PRJNA629096 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11638300.fastq.gz	Fastqsanger.gz
	SRR11638301.fastq.gz	Fastqsanger.gz
	SRR11638302.fastq.gz	Fastqsanger.gz
	SRR11638303.fastq.gz	Fastqsanger.gz
	SRR11638297_subreads.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 7

Similar Datasets

Long-TUC-seq is a robust method for quantification of metabolically labeled full-length isoforms

Project description:The steady state expression of each gene is the result of transcriptional rate, dynamic processing, and degradation of RNA. While regular RNA-seq methods only measure steady state expression levels, RNA-seq of metabolically labeled RNA identifies transcripts that were transcribed during the window of metabolic labeling. Whereas short-read RNA sequencing can identify metabolically labeled RNA at the gene level, long-read sequencing results in dramatically improved resolution of isoform-level transcription. Here we combine thiouridine-to-cytosine conversion (TUC) with PacBio long-read sequencing to study the dynamics of mRNA transcription in the GM12878 cell line. We show that using long-TUC-seq, we can detect metabolically labeled mRNA of distinct isoforms more reliably than using short reads. Long-TUC-seq holds the promise of capturing isoform dynamics robustly and without the need for enrichment.

2020-04-30 | GSE149551 | GEO

Effect of TUC-seq protocol versus SLAM-seq on quantification bias in nucleotide conversion RNA-seq data

Project description:To investigate the effect of TUC-seq versus SLAM-seq on quantification bias in nucleotide conversion RNA-seq, we performed SLAM-seq and TUC-seq on NIH cells. We then measured 4sU dropout in 4sU samples compared to 4sU naive samples.

2024-02-06 | GSE253169 | GEO

Sequencing of metabolically labeled transcripts in single cells from RPE1-FUCCI cells and murine intestinal organoids.

Project description:Measurements of metabolically labeled transcripts in single cells for estimation of mRNA synthesis and degradation rates throughout the cell cycle and intestinal organoid differentiation.

2020-03-05 | GSE128365 | GEO

Sequencing of metabolically labeled transcripts in single cells from RPE1-FUCCI cells and murine intestinal organoids.

Project description:Sequencing of metabolically labeled transcripts in single cells from RPE1-FUCCI cells and murine intestinal organoids.

| PRJNA527268 | ENA

15N-labeled full-length apolipoprotein E4 as an internal standard for mass spectrometry quantification of apolipoprotein E isoforms.

Project description:Apolipoprotein E isoforms (apoE2, apoE3, and apoE4) affect the likelihood of developing Alzheimer's disease (AD), with the apoE4 isoform being a major risk factor. However, the underlying mechanism remains to be determined. ApoE isoforms vary by a single amino acid change, and it is a challenge to distinguish them on the protein level. We developed a mass spectrometry-based quantitative method utilizing (15)N-labeled full-length apoE4 ((15)N-apoE4) as an internal standard to quantify concentrations of the specific apoE4 isoform and total apoE. The measurements were performed on control and severe AD samples from human postmortem brain in a single experimental run with a single internal standard, (15)N-apoE4. By subtracting apoE4 from total apoE, the concentration of apoE2 or apoE3 for individuals possessing ?2/?4 or ?3/?4 alleles can be assessed. Moreover, using the full-length (15)N-apoE4 standard for the set of samples with pure ?2/?2, ?3/?3, or ?4/?4 genotypes makes possible comparison of changes that occur in individual apoE2, apoE3, or apoE4 isoforms, respectively. Overall, using this method, it is possible to study the differences between apoE isoform functions on the protein level and therefore to understand the underlying biological mechanism by which apoE alters AD susceptibility.

| S-EPMC4038910 | biostudies-literature

Saccharum hybrid cultivar cultivar:TUC 95-10

Project description:Saccharum cv. TUC 95-10 Resequencing

| PRJNA1228813 | ENA

Saccharum hybrid cultivar cultivar:TUC 03-12

Project description:Saccharum cv. TUC 03-12 Resequencing

| PRJNA1228777 | ENA

Saccharum hybrid cultivar cultivar:TUC 02-22

Project description:Saccharum cv. TUC 02-22 Resequencing

| PRJNA1228693 | ENA

Klebsiella sp. Kd70 TUC-EEAOC

Project description:Klebsiella sp. Kd70 TUC-EEAOC Genome sequencing and assembly