Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RiboSeq of Interferon-β treated neural stem cells

ABSTRACT: Neural stem cells were treated with vehicle or Interferon-β for different treatment lengths. Ribosome protected RNA and total RNA were extracted and sequenced

ORGANISM(S): Mus musculus

PROVIDER: GSE193465 | GEO | 2023/01/13

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Ribosome Footprinting (RiboSeq) analysis of mRNA translation in Dis3l2 knockout mESCs

Project description:Input mRNAs and ribosome protected fragments (RPFs) from Heterozygout (Control) and Dis3l2 knockout (KO) mESCs cultures were analyzed by TruSeq Ribo Profile (Illumina) library preparation and high throughput sequencing

2020-04-04 | GSE136350 | GEO

Interferon-Beta Gene Transfer (Ad.hIFN-β) as Treatment for Refractory Colorectal Carcinoma With Liver Metastases

Project description:This study will be conducted in subjects with refractory colorectal carcinoma with unresectable liver metastases. The purposes of the study are: * to evaluate the safety and any harmful effects of an intravenous injection of Ad.hIFN-β; * help determine whether the virus carrying the interferon-beta gene will enter the bloodstream and liver tumor cells and cause the cancer cells to die.

| 2012584 | ecrin-mdr-crc

RiboSeq of BSR cells infected at MOI 3 with Theiler's murine encephalomyelitis virus, compared to mock-infected controls, harvested at 10 hpi. Fragments of lengths 35-65 nt purified.

Project description:BSR cells were infected with the Cardiovirus B archetype, Theiler’s murine encephalomyelitis virus (TMEV), and mutants thereof, and subjected to ribosome profiling to analyse ribosome collision events on the viral genome. Samples were harvested at 10 hpi by flash-freezing, without cycloheximide pre-treatment. RNase I treatment was carried out, following which ribosomes and enclosed RNA were isolated by centrifugation through a sucrose cushion. RNA was extracted, ribosomal RNA was removed using Illumina's RiboZero kit, and remaining RNA was gel purified to select fragments 35-65nt long, in order to capture fragments protected by disomes. Fragments were cloned into adapters based on the TruSeq small RNA adapter kit, with an additional seven random nucleotides at 5′-end of the 3′-adapter. Libraries were sequenced on the Illumina NextSeq 500 platform.

2021-11-10 | E-MTAB-9437 | biostudies-arrayexpress

Transcriptional program of regulatory T cells in transplanted mice treated with interferon beta

Project description:We report the differences in transcriptional program of Foxp3+ cells in mice B6 mice recipients of a BALB/c heart treated with CTLA-4 Ig and either vehicle or interferon beta (IFNb)

2021-12-20 | GSE191154 | GEO

RNAseq of Huh7 and Huh7.5 cells treated with interferon alpha, beta or lambda.

Project description:The transcriptome of Huh7 and Huh7.5 was sequenced from cells treated with interferon alpha (IFNα), beta (IFNβ) or lambda (IFNλ) for 8 hours. Each treatment was compared to respective mock-treated cells in 6 pairwise comparisons, for a total of 43 samples classified in 12 experimental conditions. Cells were treated for 8h with 10ng/ml of Interferon-α2A, 5000 U/ml of Interferon-β1A or 100ng/ml of interferon-λ3 prior RNA extraction and library preparation. Mock-treated cells were used as control for each treatment. 3 to 4 biological replicates were analysed for each biological condition. Libraries for Illumina sequencing were constructed by polyA selection with the Illumina Kit. A paired end (2x100) run was performed.

2021-08-17 | E-MTAB-10469 | biostudies-arrayexpress

Translation of Circular RNAs in Neural Retina

Project description:We performed Ribosome-protected mRNA fragment sequencing (Ribo-Seq) to determine if retinal circular RNAs are undergoing translation

2022-02-14 | GSE166919 | GEO

RNA-seq of monocyte derived macrophages exposed to arachidonic acid, interferon beta, or interferon gamma

Project description:Monocyte derived macrophages were exposed to arachidonic acid, interferon beta, or interferon gamma

2021-12-31 | E-MTAB-10867 | biostudies-arrayexpress

Sequence selectivity of macrolide-induced translational regulation

Project description:We sequenced a total of 12 cDNA libararies derived from fragmented total mRNA and ribosome protected mRNAs from azithromycin-treated and -untreated S. aureus samples. The data represented 2 independent biological replicates. Examination of the impact of azithromycin on global translatome, mRNA abundance and the ribosome density along the transcripts.

2014-11-03 | E-GEOD-57175 | biostudies-arrayexpress

Sequence selectivity of macrolide-induced translational regulation

2014-11-03 | GSE57175 | GEO

smORF atlas (part 1-RiboSeq)

Project description:Small open reading frames (smORFs) can have important regulatory roles and give rise to stable proteins, yet their discovery based on sequence-based predictions and proteomics has been challenging. Ribosome profiling (Ribo-seq) data can provide valuable experimental evidence of RNA translation. Stringent analysis of P-sites, representing 1.3 billion high-confidence ribosome locations, revealed 5308 uORFs, 1652 smORFs in lincRNAs and 807 dORFs that are translated in humans. We here provide a comprehensive database of Ribo-seq smORFs for a more complete understanding of the translated human genome.

2022-07-18 | GSE182371 | GEO

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