Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Guidelines for performing Ribosome Profling in Plants Including Structural Analysis of rRNA fragments

ABSTRACT: Guidelines for performing Ribosome Profling in Plants Including Structural Analysis of rRNA fragments

PROVIDER: PRJNA940452 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23689209.fastq.gz	Fastqsanger.gz
	SRR23689210.fastq.gz	Fastqsanger.gz
	SRR23689211.fastq.gz	Fastqsanger.gz
	SRR23689212.fastq.gz	Fastqsanger.gz
	SRR23689213.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Guidelines for performing Ribosome Profling in Plants Including Structural Analysis of rRNA fragments

Project description:Here, we compile valuable insights gathered over years of generating Ribo-seq datasets from different plant species and experimental setups. We tested the effects of variable ribonuclease treatments for the generation of ribosome protected fragments (RPFs). We tested rRNA depletion strategies designed specifically for Arabidopsis and Tobacco. We also compare ligation-free to ligation-based library preparation strategies for generating Ribo-seq libraries.

2024-07-05 | GSE226508 | GEO

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

Project description:Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. We present a protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing. This ribosome profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. Additionally, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, we describe an adaptation that reveals the sites of translation initiation by pre-treating cells with harringtonine to immobilize initiating ribosomes. The protocol we describe requires 5 - 7 days to generate a completed ribosome profiling sequencing library. Ribosome profiling in cultured mammalian cells under three different footprinting conditions

2012-07-26 | E-GEOD-37744 | biostudies-arrayexpress

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

2012-07-26 | GSE37744 | GEO

VTA and NAC labeled ribosome from mPFC

Project description:Projection-dependent ribosome profling from mouse mPFC. Ribosome from NAC- and VTA- projecting mPFC cells were immunoprecipited using GFP-trap (Chromotech). Translating mRNA was isolated and analyzed

2017-09-15 | GSE101185 | GEO

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

Project description:During translation elongation, the ribosome ratchets along its mRNA template, incorporating each new amino acid and translocating from one codon to the next. The elongation cycle requires dramatic structural rearrangements of the ribosome. We show here that deep sequencing of ribosome-protected mRNA fragments reveals not only the position of each ribosome but also, unexpectedly, its particular stage of the elongation cycle. Sequencing reveals two distinct populations of ribosome footprints, 28-30 nucleotides and 20-22 nucleotides long, representing translating ribosomes in distinct states, differentially stabilized by specific elongation inhibitors. We find that the balance of small and large footprints varies by codon and is correlated with translation speed. The ability to visualize conformational changes in the ribosome during elongation, at single-codon resolution, provides a new way to study the detailed kinetics of translation and a new probe with which to identify the factors that affect each step in the elongation cycle. Ribosome profiling, or sequencing of ribosome-protected mRNA fragments, in yeast. We assay ribosome footprint sizes and positions in three conditions: untreated yeast (3 replicates) and yeast treated with translation inhibitors cycloheximide (2 replicates) and anisomycin (2 biological replicates, one technical replicate). We also treat yeast with 3-aminotriazole to measure the effect of limited histidine tRNAs on ribosome footprint size and distribution (two treatment durations).

2014-06-10 | E-GEOD-58321 | biostudies-arrayexpress

tRNAArg-derived fragments mediate protein arginylation

Project description:tRNAArg-derived fragments mediate protein arginylation

| PRJNA610185 | ENA

Analysis of Ribosome Protected Fragments of mRNAs from yeast strains either expressing Rio1p or depleted of Rio1p

Project description:mRNAs bound by ribosomes from yeast cells were analysed in order to determine the exact position of ribosomes in the presence or absence of Rio1p. Beside total Ribosome Protected Fragments (RPFs), RPFs from mRNAs protected by immature pre-40S pre-ribosomes was also analysed. The analysis showed that immature 40S ribosomes can carry out translation and their premature entry into translation is hindered by Rio1p.

2017-08-16 | GSE98333 | GEO

Transcriptome Analyses in BV2 microglial cells following treatment with amino-terminal fragments of apolipoprotein E

Project description:This study assessed the effects of amino terminal ApoE4 fragments (residues 1-151) on modulating the transcriptome of BV2 microglial cells. Treatment with amino terminal ApoE4 fragments caused the upregulation of nearly four-thousand genes, and further analysis revealed a significant upregulation of genes related to the inflammatory immune response. As a control, an amino terminal ApoE3 fragment was tested and produced a similar but reduced level of upregulation of an identical set of genes. This set of genes affected pathways including Toll receptor signaling, chemokine/cytokine signaling and apoptosis signaling. Additionally, each treatment regulated a unique set of genes. Amino terminal ApoE3 fragments uniquely regulated 14 times as many genes (1,674), many of which are involved in physiological functions within microglia. Amino terminal ApoE4 fragments uniquely upregulated 119 genes, with many of the top upregulated genes having unknown functions. Our results suggest that while amino terminal ApoE3 fragments may serve a more physiological role in microglia amino terminal ApoE4 fragments may activate genes with a more pathological purpose. These data support the hypothesis that the link between harboring the APOE4 allele and dementia risk could be enhanced inflammation through activation of microglia.

2020-07-31 | GSE153454 | GEO

Transcriptional profile of human macrophages stimulated by cartilage fragments

Project description:Accumulating evidence suggests that synovitis is associated with osteoarthritic process. Macrophages are predominant cell type in synovium and play principal role in development of synovitis. Our earlier study suggests that the interaction between cartilage fragments and macrophages exacerbates osteoarthritic process. However, molecular mechanisms by which cartilage fragments trigger cellular responses remain to be investigated. Therefore, the current study aims at analyzing molecular response of macrophages to cartilage fragments by RNA-seq

2020-05-13 | GSE141308 | GEO

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

2014-06-10 | GSE58321 | GEO