Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ribosome profiling of H9 PUS7KO

ABSTRACT: Ribosome profiling of H9 PUS7KO

PROVIDER: PRJNA680364 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13120317.fastq.gz	Fastqsanger.gz
	SRR13120318.fastq.gz	Fastqsanger.gz
	SRR13120319.fastq.gz	Fastqsanger.gz
	SRR13120320.fastq.gz	Fastqsanger.gz
	SRR13120321.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Ribosome profiling of MCMV

Project description:Ribosome profiling of MCMV

| PRJNA874814 | ENA

Ribosome profiling in cyanobacteria

Project description:Ribosome profiling in cyanobacteria

| PRJEB28203 | ENA

Ribonuclease Selection for Ribosome Profiling

Project description:Ribosome profiling has emerged as a powerful method to assess global gene translation, but methodological and analytical challenges often lead to inconsistencies across labs and model organisms. A critical issue in ribosome profiling is nuclease treatment of ribosome-mRNA complexes, as it is important to ensure both stability of ribosomal particles and complete conversion of polysomes to monosomes. We performed comparative ribosome profiling in yeast and mice with various ribonucleases including I, A, S7 and T1, characterized their cutting preferences, trinucleotide periodicity patterns, and coverage similarities across coding sequences, and showed that they yield comparable estimations of gene expression when ribosome integrity is not compromised. However, ribosome coverage patterns of individual transcripts had little in common between the ribonucleases. We further examined their potency at converting polysomes to monosomes across other commonly used model organisms, including bacteria, nematodes and fruit flies. In some cases, ribonuclease treatment completely degraded ribosome populations. Ribonuclease T1 was the only enzyme that preserved ribosomal integrity while thoroughly converting polysomes to monosomes in all examined species. This study provides a guide for ribonuclease selection in ribosome profiling experiments across most common model systems

2016-09-20 | GSE82220 | GEO

Pseudomonas sp. H9 strain:H9

Project description:Pseudomonas sp. H9 strain:H9 Genome sequencing and assembly

| PRJNA526342 | ENA

Roseobacter sp. H9 strain:H9

Project description:Roseobacter sp. H9 strain:H9 Genome sequencing and assembly

| PRJNA657503 | ENA

Ribonuclease Selection for Ribosome Profiling

Project description:Ribonuclease Selection for Ribosome Profiling

| PRJNA324380 | ENA

Ribosome profiling of LS180 cells

Project description:Ribosome profiling of LS180 cells

| PRJNA870767 | ENA

Ribosome Profiling of Mycobacterium smegmatis

Project description:Ribosome Profiling of Mycobacterium smegmatis

| PRJEB7261 | ENA

Ribosome Profiling with CNOT1 depletion

Project description:Ribosome Profiling with CNOT1 depletion

| PRJNA664116 | ENA

Bacterial ribosome pause sites surveyed by an integration of ribosome profiling and nascent chain profiling II

Project description:Ribosome pauses are associated with diverse co-translational events and determine the fate of mRNAs and proteins. Thus the identification of the precise pause sites across transcriptome is a key, however, the landscape in bacterial has remained ambiguous. Here, we harnessed the multiple ribosome profiling strategies (standard, high-salt-wash, and disome) to survey the robust ribosome pause sites in E. coli. The found pause sites showed the correspondence with biochemical validation by integrated nascent chain profiling (iNP), which detects polypeptidyl-tRNA, an elongation intermediate. Among the list, ribosome pause at Asn586 of ycbZ was ensured by biochemical reporter assay, tRNA-seq, and cryo-electron microscopy. Our results provide a useful resource of ribosome stalling sites in bacteria.

2021-11-23 | GSE180482 | GEO

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