Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

45 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of cardiovirus and infected host-cell gene expression through RNA sequencing and ribosome profiling

ABSTRACT: Ribosome profiling (RiboSeq) (maps positions of translating ribosomes on the transcriptome) and RNASeq (quantifies the transcriptome) analysis of murine L929 cells infected with encephalomyocarditis virus vMC0. Samples comprise 2, 4, 6 and 8 h post infection RiboSeq timecourses for WT virus and a shift mutant [SS] (8 samples), and RiboSeq and RNASeq at 8 h post infection for WT virus and 5 mutant viruses (shift site [SS], stem-loop [WT-SL], shift site and stem-loop [SS-SL], StopGo [LV], and StopGo, shift site and stem-loop [LV-SS-SL]) (12 samples).

INSTRUMENT(S): NextSeq 500, Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER: Andrew Firth

PROVIDER: E-MTAB-5206 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling

Project description:Ribosome profiling (RiboSeq) (maps positions of translating ribosomes on the transcriptome) and RNASeq (quantifies the transcriptome) analysis of murine 17 clone 1 (17Cl-1) cells infected with Murine coronavirus strain A59 (MHV-A59). Samples comprise 1 and 8 h mocks, 1, 2.5, 5 and 8 h post infection timecourse, for each of RiboSeq with cycloheximide (CHX), RiboSeq with harringtonine (HAR), and RNASeq, performed in duplicate (6 x 3 x 2 libraries); RiboSeq CHX, RiboSeq HAR and RNASeq at 1 h post infection for high multiplicity of infection (3 libraries); and 1 \long-read\ library for 5 h post infection RiboSeq CHX to test for larger-than-normal ribosome footprints.

2016-02-08 | E-MTAB-4111 | biostudies-arrayexpress

Ribosome profiling of Tunicamycin-treated and -untreated 17Cl1 cells

Project description:Ribosome profiling (RiboSeq) analysis of murine 17 clone 1 (17Cl-1) cells with and without Tunicamycin treatment. Tunicamycin is known to induce the unfolded protein response, and the objective of this work was to assess the impact of Tunicamycin on cellular translation. Additionally, we sought to assess the impact of differing library preparation methods by using three separate approaches: flash freezing, 1X Cycloheximide, and 100X Cycloheximide.

2021-11-09 | E-MTAB-5391 | biostudies-arrayexpress

Paired-end ribosome profiling of MARC-145 cells infected with porcine reproductive and respiratory syndrome virus (PRRSV)-2, harvested at 9 hpi

Project description:MARC-145 cells were infected with porcine reproductive and respiratory syndrome virus (PRRSV)-2 isolate SD95-21 (KC469618.1), and a mutant thereof (KO2), and subjected to ribosome profiling to analyse the viral and host translatome, frameshifting on the viral genome, and putative frameshift-related ribosome pausing events. Samples were harvested at 9 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 19-80nt long. Fragments were cloned into adapters based on the TruSeq small RNA adapters, with an additional seven random nucleotides at the 5′-end of the 3′-adapter and the 3′-end of the 5′-adapter. Libraries were sequenced on the Illumina NextSeq 500 platform as a paired-end run. Note that sample nomeclature (including replicate numbers) is consistent between this and the two related accessions, and RiboSeq libraries are matched with RNASeq libraries, which were prepared from the same lysate.

2022-03-09 | E-MTAB-10622 | biostudies-arrayexpress

Ribosome profiling of the retrovirus murine leukemia virus

2018-01-17 | E-MTAB-6231 | biostudies-arrayexpress

Ribosome profiling of mouse hepatitis virus (MHV)-infected and uninfected 17Cl1 cells

Project description:Ribosome profiling (RiboSeq) analysis of murine 17 clone 1 (17Cl-1) cells with and without MHV infection. We sought to assess the impact of differing library preparation methods by using three separate approaches: flash freezing, 1X cycloheximide pretreatment, and 100X cycloheximide pretreatment.

2021-11-09 | E-MTAB-6278 | biostudies-arrayexpress

Analysis of Zika Virus gene expression by Ribosome profiling and RNA sequencing

Project description:Ribosome profiling (Ribo-Seq) (maps positions of translating ribosomes on the transcriptome) and RNA-Seq (quantifies the transcriptome) analysis of African green monkey (Vero E6) cells and Aedes albopictus (C6/36) cells infected with Zika Virus (ZIKV) strain PE243. Cells were harvested at 24 h post infection (p.i.) and Ribo-Seq and RNA-Seq libraries were prepared and deep sequenced.

2018-06-30 | E-MTAB-5418 | biostudies-arrayexpress

RNASeq of African green monkey (Vero) cells infected at a multiplicity of infection (MOI) of 3 with the African Zika virus (ZIKV) strain, Dak84. A contamination with Toscana virus (TOSV) was discovered during bioinformatic analysis

Project description:Vero cells were infected with the African ZIKV (Dak84) at MOI:3 to assess the viral transcriptome. Samples were harvested at 24 hours post-infection (h p.i.) by flash-freezing, without cycloheximide pre-treatment. Ribosomal RNA was removed using Illumina's RiboZero kit, and RNA was hydrolysed and then gel purified to select fragments 25-35nt long. Fragments were cloned into adapters using the TruSeq small RNA adapter kit and sequenced on Illumina NextSeq. After bioinformatic analysis, it was discovered that infected cells were contaminated with another arbovirus, Toscana virus (TOSV).

2024-11-08 | E-MTAB-14056 | biostudies-arrayexpress

RNASeq of African green monkey (Vero) cells infected at a multiplicity of infection (MOI) of 3 with different Zika virus (ZIKV) mutants (American WT, African-like, uORF1-KO and uORF2-PTC1) generated by reverse genetics

Project description:Vero cells were infected with the different Zika virus (ZIKV) mutants (American WT, African-like, uORF1-KO and uORF2-PTC1) generated by reverse genetics at MOI:3 to assess their viral transcriptome. Samples were harvested at 24 hours post-infection (h p.i.) by flash-freezing, without cycloheximide pre-treatment. Ribosomal RNA was removed using Illumina's RiboZero kit, and RNA was hydrolysed and then gel purified to select fragments 25-35nt long. Fragments were cloned into adapters using the TruSeq small RNA adapter kit and sequenced on Illumina NextSeq.

2024-09-04 | E-MTAB-12968 | biostudies-arrayexpress

RNASeq of murine 17Cl-1 cells infected at MOI 10 with MHV-A59, compared to mock-infected controls, harvested at 5 and 8 hpi.

Project description:Murine 17Cl-1 cells were infected with the model Betacoronavirus mouse hepatitis virus (MHV) strain A59 to observe changes in the host transcriptome in infected cells compared to mock-infected cells. Samples were harvested at 5 and 8 hpi by flash-freezing, without cycloheximide pre-treatment. Ribosomal RNA was removed using Illumina's RiboZero kit, and RNA was hydrolysed then gel purified to select fragments 25-35nt long. Fragments were cloned into adapters using the TruSeq small RNA adapter kit and sequenced on Illumina NextSeq, then differential gene expression analysis was carried out on the data deposited data.

2021-05-18 | E-MTAB-8651 | biostudies-arrayexpress

RiboSeq of African green monkey (Vero) cells infected at a multiplicity of infection (MOI) of 3 with the Asian/American Zika virus (ZIKV) strain, PE243

Project description:Vero cells were infected with the Asian/American Zika virus (ZIKV) strain, PE243, at MOI:3 to assess the viral transcriptome. Samples were harvested at 24 hours post-infection (h p.i.) 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 25-35nt long. Fragments were cloned into adapters using the TruSeq small RNA adapter kit and sequenced on Illumina NextSeq.

2024-09-04 | E-MTAB-12971 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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