Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

77 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ribo_seq (aka ribosome profiling) analysis of control and Myc-induced U2OS cells

ABSTRACT: We used Ribo-seq to examine the effect of Myc activation on protein translation in U2OS cells and correalted these changes with alterations in RNA level measured by RNA-seq on tye same conditions. We also examined these effects in the presence of Torin-1, an inhibitor of mTOR We measure ribosome occupancy profiles in U2OS cells containing an inducible Myc expression vector that were induced or mock-treated in duplicates for 36 hours. In addition, we repeated the experiments in the presence of Torin-1, an inhibitor of mTOR.

ORGANISM(S): Homo sapiens

SUBMITTER: Ran Elkon

PROVIDER: E-GEOD-66927 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Ribosome profiling and RNA sequencing of MCF10A cells treated with torin or by serum starvation

Project description:MCF10A were either untreated, treated with torin or by starvation, to induce autophagy. RNA sequencing and ribosome profiling was performed. 1 biological replicate for each condition

2016-02-17 | E-GEOD-59816 | biostudies-arrayexpress

ASNase treatment in PC3 cells

Project description:Ribosome profiling performed on control and L-Asparaginase treated PC3 cells 2 individual batches: (i) 1 control and 1 treated sample, (ii) 1 control and 2 treated samples

2016-02-17 | E-GEOD-74510 | biostudies-arrayexpress

Myc activation coordinates gene transcription and protein translation responses

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-11-04 | E-GEOD-66929 | biostudies-arrayexpress

Ribosome profiling on glutamine-starved panel of luminal and basal breast cancer cell lines

Project description:Four different breast cancer cell lines were grown either under unrestricted growth conditions or in medium lacking glutamine, and ribosome profliling was performed on material extracted from these samples 1 replicate per condition

2016-02-17 | E-GEOD-69923 | biostudies-arrayexpress

Ribosome profiling on sections taken from a kidney tumor

Project description:Ribosome profiling on sections taken from a kidney tumor For two tumors: 2 sections of normal tissue and 4 samples of tumor tissue, for another two tumors 1 section of normal tissue and 1 section of tumor tissue

2016-02-17 | E-GEOD-59820 | biostudies-arrayexpress

Restrictions in amino acid availability revealed by differential ribosome codon reading

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-02-14 | E-GEOD-59821 | biostudies-arrayexpress

Ribosome profiling on polysomes extracted via sucrose gradient and IP

Project description:Technical feasibility study to determine data quality and reproducibilty. Ribosome profiling was performed by either sucrose gradient (SG) or immunoprecipitation (IP). 1 sucrose gradient sample, 2 immunoprecipitation samples in two concentrations of beads

2016-02-17 | E-GEOD-74511 | biostudies-arrayexpress

Ribosome profiling on SUM159PT cells grown in vitro or in vivo

Project description:SUM159PT cells were grown either in vitro (in culture) or in vivo (mouse), after which RPL10a tagged with GFP was used to perform extraction by immoprecipitation and subsequent ribosome profiling Two batches of in vitro grown cells, each having 2 replicates. Two batches of in vivo grown cells from tumors grown in two individual mice, each having tumors on left (first batch) and right side (second batch). Extraction and ribosome profiling was done independently for the two batches of samples.

2016-02-17 | E-GEOD-74512 | biostudies-arrayexpress

Meiotic double-strand break end resection mapping by S1Seq

Project description:The DNA double-strand breaks that initiate homologous recombination during meiosis are subject to extensive 5Ê¹â??3â?² exonucleolytic processing. This resection is a central and conserved feature of recombination, yet its mechanism is poorly understood. Using a purpose-made deep-sequencing method, namely S1Seq, we mapped meiotic resection endpoints genome-wide at high spatial resolution in Saccharomyces cerevisiae. Generating full-length resection tracts requires Exo1 exonuclease activity and the DNA-damage responsive kinase Tel1, but not the helicase Sgs1. Tel1 is also required for efficient and timely initiation of resection. We find that distributions of resection endpoints at individual genomic loci display pronounced heterogeneity that reflects a tendency for nucleosomes to block Exo1 in vivo, yet modeling experiments indicate that Exo1 digests chromatin with high apparent processivity and at rates approaching those for naked DNA in vitro. This paradox points to nucleosome destabilization or eviction as a determining feature of the meiotic resection landscape. 36 samples total: two biological replicate S1Seq maps of S.cerevisiae for each genetic background and time point in meiosis

2016-08-06 | E-GEOD-85253 | biostudies-arrayexpress

Global analysis of pre-mRNA subcellular localization upon splicing inhibition by spliceostatin A

Project description:RNA-Seq analysis of SSA treated cells HeLa cells, nuclear and cytoplasmic fractions, treated with SSA or MeOH

2016-02-17 | E-GEOD-72156 | biostudies-arrayexpress