Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ribosomal footprinting of MDA-Parental and MDA-LM2

ABSTRACT: We used Illlumina Artseq Ribo Profile to perform ribosome footprinting on the above cell lines

ORGANISM(S): Homo sapiens

PROVIDER: GSE77315 | GEO | 2016/06/07

SECONDARY ACCESSION(S): PRJNA310015

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Ribosomal footprinting of CN34-Parental and CN34-LM1a

Project description:We used Illlumina Artseq Ribo Profile to perform ribosome footprinting on the above cell lines

2016-06-07 | GSE77292 | GEO

Ribosomal footprinting of MDA_Ctrl and MDA_Glu overexpression cell lines

Project description:We used Illlumina Artseq Ribo Profile to perform ribosome footprinting on the above cell lines

2016-06-07 | GSE77347 | GEO

Ribosomal footprinting of MDA_Ctrl and MDA_Arg overexpression cell lines

Project description:We used Illlumina Artseq Ribo Profile to perform ribosome footprinting on the above cell lines

2016-06-07 | GSE77317 | GEO

RNA sequencing of MDA-LM2 and MDA-Parental cells

Project description:We used RNA sequencing to compare MDA-MB-231 cells to their higly metastatic MDA-LM2 derivatvies.

2021-03-30 | GSE160953 | GEO

Analysis of HNRNPC Interactome in MDA-MB231 parental and LM2 cells

Project description:To define and compare the interactomes of the RNA binding protein HNRNPC in poorly vs. efficiently metastatic breast adenocarcinoma cells, we carried out immunoprecipitation of endogenous HNRNPC from parental MDA-MB231 cells vs. its highly metastatic isogenic derivate, the MDA-MB231-LM2 cells. We used a non-specific MOUSE IgG IP from each line as control. Each IP was performed in triplicate, and analysed by LC-MS/MS, on a Thermo Q-Exactive-plus instrument.

2023-02-19 | PXD029560 | Pride

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

Project description:So far, the annotation of translation initiation sites (TISs) has been based mostly upon bioinformatics rather than experimental evidence. We adapted ribosomal footprinting to puromycin-treated cells to generate a transcriptome-wide map of TISs in a human monocytic cell line. A neural network was trained on the ribosomal footprints at previously annotated AUG translation initiation codons (TICs), and used for the ab initio prediction of TISs in 5062 transcripts with sufficient sequence coverage. Functional interpretation suggested 2994 novel upstream open reading frames (uORFs) in the 5´ UTR (924 AUG, 2070 near-cognate codons), 1406 uORFs overlapping with the coding sequence (116 AUG, 1290 near-cognate) and 546 N-terminal protein extensions (6 AUG, 540 near-cognate). The TIS detection method was validated on the basis of previously published alternative TISs and uORFs. On average, TICs in newly annotated TISs were significantly more conserved among primates than control codons, both for AUGs (p<10-10) and near-cognate codons (p=3.8×10-3). The derived transcriptome-wide map of novel candidate TISs will help to explain how human proteome diversity is influenced by alternative translation initiation and regulation. Examination of translational initiation in human cell lines using ribosomal footprinting

2012-08-08 | E-GEOD-39561 | biostudies-arrayexpress

Ribosomal footprinting and RNASeq in two strains of yeast and their diploid hybrid

Project description:Heritable differences in gene expression between individuals are an important source of phenotypic variation. The question of how closely the effects of genetic variation on protein levels mirror those on mRNA levels remains open. Here, we addressed this question by using ribosomal footprinting to examine how genetic differences between two strains of the yeast S. cerevisiae affect translation. Strain differences in translation were observed for hundreds of genes, more than half as many as showed genetic differences in mRNA levels. Similarly, allele specific measurements in the diploid hybrid between the two strains found roughly half as many cis-acting effects on translation as were observed for mRNA levels. In both the parents and the hybrid, strong effects on translation were rare, such that the direction of an mRNA difference was typically reflected in a concordant footprint difference. The relative importance of cis and trans acting variation on footprint levels was similar to that for mRNA levels. Across all expressed genes, there was a tendency for translation to more often reinforce than buffer mRNA differences, resulting in footprint differences with greater magnitudes than the mRNA differences. Finally, we catalogued instances of premature translation termination in the two yeast strains. Overall, genetic variation clearly influences translation, but primarily does so by subtly modulating differences in mRNA levels. Translation does not appear to create strong discrepancies between genetic influences on mRNA and protein levels. Ribsosomal footprinting and RNASeq in the two yeast strains BY and RM as well as their diploid hybrid. We generated one library each for the BY and RM parents, and two libraries (biological replicates) for the hybrid data.

2014-03-31 | E-GEOD-55400 | biostudies-arrayexpress

RNA sequencing of MDA-LM2 and MDA-Parental cells

Project description:RNA sequencing of MDA-LM2 and MDA-Parental cells

| PRJNA674896 | ENA

Ribosome footprinting of fly heads

Project description:We applied ribosomal footprinting experiment followed by RNA-seq in order to detect circular RNA associated with ribosomes in fly heads.

2017-03-24 | GSE79626 | GEO

Nanoparticles and photochemistry for Native-like transmembrane protein footprinting

Project description:Mass spectrometry based footprinting can probe higher order structure of proteins. We bond photocatalytic nanoparticles to a lipid bilayer that, upon laser irradiation, produce high local concentrations of radicals that penetrate the lipid layer made permeable by a simultaneous laser-initiated PB reaction. This approach achieves high footprinting coverage for membrane proteins in liposomes, helps locate both ligand-binding residues in a transporter and ligand-induced conformational changes, and reveals structural aspects of the flexible unbound state. Overall, this approach proves highly effective in intramembrane footprinting and forges a connection between materials science and biology.

2021-09-26 | PXD027819 | Pride

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