Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq of ribosomal footprints

ABSTRACT: Cancer genes can affect ribosomal RNA processing and this can underlie their essentiality to cells, making them cell-essential in the same way as ribosomal genes themselves. We want to confirm this, in order to understand the results of our CRISPR drop-out screens. NOTE FROM BESPOKE TEAM: Run a single read 1 (forward read) of 30 bases, then an index 1 read as normal. This would fit a 50cycle kit

PROVIDER: EGAS00001001591 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

RNAseq of ribosomal footprints

Project description:Cancer genes can affect ribosomal RNA processing and this can underlie their essentiality to cells, making them cell-essential in the same way as ribosomal genes themselves. We want to confirm this, in order to understand the results of our CRISPR drop-out screens.NOTE FROM BESPOKE TEAM: Run a single read 1 (forward read) of 30 bases, then an index 1 read as normal. This would fit a 50cycle kit

2016-05-18 | E-ERAD-444 | biostudies-arrayexpress

EGAS00001001591-sc-20160224 - samples

Project description:Cancer genes can affect ribosomal RNA processing and this can underlie their essentiality to cells, making them cell-essential in the same way as ribosomal genes themselves. We want to confirm this, in order to understand the results of our CRISPR drop-out screens. NOTE FROM BESPOKE TEAM: Run a single read 1 (forward read) of 30 bases, then an index 1 read as normal. This would fit a 50cycle kit

| EGAD00001001930 | EGA

Project description:Forward genetic screens Arthrobotrys oligospora mutants

| PRJNA670551 | ENA

Human miRNA expression in EBV+ and EBV- PTLD tumor tissue sections

Project description:Expression of human miRNAs was analyzed in 150 ng of total RNA from nine post-transplant lymphoproliferative disorder (PTLD) patient samples, categorized as Epstein-Barr virus-positive (EBV+ , n = 4) or EBV- (n = 5) PTLD by hybridization on Affymetrix’s GeneChip miR Array 4.0 (Stanford Functional Genomics Facility, Stanford, CA). The Bioconductor ‘oligo’ package was used to perform array background subtraction, quantile normalization, and summarization by median polish. The normalized gene expression dataset was annotated with the ‘pd.mirna.4.0’ annotation library package in R (R Core Team). The expression data was fit to a linear model using the ‘stats’ package in R (R Core Team). Moderated t-statistics and log-odds of differential expression were calculated using the empirical Bayes method. False discovery rate (FDR) tests were performed with the Benjamini-Hochberg procedure for multiple testing correction in R (R Core Team).

2022-10-31 | E-MTAB-12201 | biostudies-arrayexpress

Role of eEF2 diphthamide modification in translational fidelity

Project description:Diphthamide (DPH) is a conserved amino acid modification on eukaryotic translation elongation factor eEF2. We show that loss of DPH increases -1 ribosomal frameshifting at both programmed, including in SARS-CoV-2, and non-programmed sites. Ribosome profiling of yeast and mammalian cells lacking DPH reveals increased ribosomal drop-off during elongation. The drop-off defect on the long yeast MDN1 gene was suppressed by eliminating out-of-frame stop codons. Our data reveal that loss of DPH impairs the fidelity of translocation during translation elongation resulting in increased rates of ribosomal frameshifting and premature termination at out-of-frame stop codons.

2023-01-10 | GSE176169 | GEO

Massively parallel genetic resistance screens

Project description:Here we describe the use of multiple forward genetic screens executed in parallel to identify those genes, and their cognate pathways, that when overexpressed, silenced or mutated confer resistance in BRAF mutant colon cancer to a BRAF/MEK/EGFR inhibitor combination. We demonstrate that this resistance landscape is finite, relatively constrained to a small number of pathways and that it is possible to exploit the evolutionary dynamics that underpins the clonal expansion of drug resistant cells therapeutically.

2022-03-23 | PXD007781 | Pride

Genetic landscape of T cells identifies synthetic lethality for T-ALL

Project description:We conducted a ENU forward genetic screen in zebrafish; identifying 42 genes differentially regulating rag1-expressing T cells fitness relative to growth hormone-expressing somatotrophic epithelials. Our forward genetic screens in zebrafish for recessive mutations affecting early T cell development revealed several major genetic pathways. Genes encoding proteins required for DNA repair & replication, cell cycle regulation, pre-mRNA processing, protein processing in the ER, ribosome biogenesis and hematopoiesis were enriched in the collection of mutants identified. To examine the molecular consequences of these mutations, bulk RNAseq was conducted on mutant and sibling wildtype embryos at 5 day post-fertilisation.

2021-10-06 | GSE147555 | GEO

RNA-seq of Malassezia sympodialis

Project description:This data set is part of a study where the genome of Malassezia sympodialis (strain ATCC 42132) was sequenced using long-read technology and annotated using RNA-seq and proteogenomics. RNA was extracted at two different culture times (2 and 4 days). Seven RNA-seq libraries were prepared from independent samples. Two samples (P2 and P3) were enriched for protein-coding RNA using poly(A)-selection. The remaining five samples were processed with RiboMinus to deplete ribosomal RNA, and thus retain both mRNA and non-ribosomal noncoding RNA for sequencing. In total, we obtained 71 million RNA-seq read pairs mapping to genomic regions other than the highly expressed ribosomal loci.

2017-01-10 | E-MTAB-4589 | biostudies-arrayexpress

Genome-wide CRISPR screen for regulators of SARS-CoV-2 programmed ribosomal frameshifting

Project description:Genome-wide CRISPR-Cas9 knockout screens were performed in dual-fluorescent frameshifting reporter cell lines to identify human host factors for SARS-CoV-2 programmed ribosomal frameshfiting.

2022-12-22 | GSE206101 | GEO

Evaluation of the Efficacy of National Cancer Institute’s Facing Forward Booklet in the Cancer Community Setting

Project description:This study was designed to provide a preliminary evaluation of the efficacy and usability of the 2004 revised version of the booklet, Facing Forward , Life After Cancer Treatment, (hereafter,Facing Forward) published by the National Cancer Institute. Facing Forward provides early stage cancer patients during the period after completing active treatment practical ways of dealing with common problems, including guidelines for managing physical, social, and emotional health. Assessments were completed at the patient’s final cancer treatment visit. Follow-up assessments occurred eight weeks and 6 months later. The initial assessments covered background information (demographics, medical status), use of educational materials, survivorship activities, and psychological factors. The follow-up assessments included use of actions recommended in Facing Forward, ratings of Facing Forward with respect the booklet’s informativeness, helpfulness, understandability, and extent read, the same psychological measures used initially, and a measure of self-efficacy.

| 2113323 | ecrin-mdr-crc

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