Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DMS probing of and sequencing of the EBV infected BJAB-B1 transcriptome

ABSTRACT: DMS probing of and sequencing of the EBV infected BJAB-B1 transcriptome

PROVIDER: PRJNA865760 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR20801866.fastq.gz	Fastqsanger.gz
	SRR20801867.fastq.gz	Fastqsanger.gz
	SRR20801868.fastq.gz	Fastqsanger.gz
	SRR20801869.fastq.gz	Fastqsanger.gz
	SRR20801870.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

DMS probing of and sequencing of the EBV infected BJAB-B1 transcriptome

Project description:To gain in cellulo, experimentally derived RNA structural information within the BJAB-B1 transcriptome

2022-08-06 | GSE210478 | GEO

MeRIP sequencing analysis of BJAB cell line infected with EBV

Project description:Purpose: Evaluation of the m6A modification of EBV and BJAB transcripts during EBV infection Methods: Human B lymphoma cell line BJAB was uninfected or infected with EBV for 24 hours. Total RNA from each sample were extracted. Intact mRNA was isolated from total RNA samples and then chemically fragmented to 100-nucleoside-long fragments. m6A methylated mRNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody (a part of the fragmented mRNAs was kept as input). Both m6A enriched mRNAs and input mRNAs were concentrated for RNA-seq library construction. Sequencing was performed using an Illumina HiSeq 4000. Results: EBV EBNA2 and BHRF1 transcripts were m6A modified and m6A modification of BJAB transcripts changed during EBV infection. Conclusions: Our study found that some EBV transcripts were m6A modified during EBV infection and EBV infection changed m6A modification profiles of BJAB transcripts.

2021-07-10 | GSE133936 | GEO

Global transcriptome analysis of BJAB cells that are modulated by EBV infection or (and) EBV BART6-3p mimics.

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using transcriptome profiling (RNA-seq) to evaluate the effects of EBV infection or (and) EBV BART6-3p mimics on the global transcriptome of the BJAB cells. Methods: BJAB cells were transfected with negative control mimics or BART6-3p mimics for 48 h and then infected with EBV virons for 2h. RNAs were extracted by Trizol and sequenced by Solexa high-throughput sequencing service (Oebiotech, Shanghai, China). Data were extracted and normalized according to the manufacturer’s standard protocol. Results: Log-fold changes of up- or down-regulated mRNAs between the control and experiment group were selected with a significance threshold of p<0.05. There are 408 mRNAs were up-regulated and 263 were down-regulated in “EBV infection” group cells comparing to “Mock” group cells. There are 385 mRNAs were up-regulated and 246 were down-regulated in “EBV infection + Bart6-3p mimics” group cells comparing to “EBV infection + negative control mimics” group cells. Conclusions: Our study describes the global transciptome changes of BJAB cells induced by EBV infection or (and) EBV 6-3p mimics.

2018-07-01 | GSE95634 | GEO

Probing in vivo RNA structure with optimized DMS-MaPseq in rice

Project description:Here, we use dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to conduct a target-specific and genome-wide profile of in vivo RNA secondary structure in rice (Oryza sativa). Our study presents an optimized DMS-MaPseq for probing in vivo RNA structure in rice.

2022-04-05 | GSE197245 | GEO

Targeted DMS probing of SF3A3 5' UTR

Project description:To delineate the native structure of SF3A3 5'UTR, RNA was harvested from IMR90 human fibroblasts. Using specific primers and DMS-MaPSeq pipeline, we validated individual base pairing probabilities within the endogenous 5'UTR of SF3A3 (samples described as 'in vivo' transcribed). DMS-MaP-Seq is based on the principle that DMS is highly reactive to solvent-accessible, unpaired adenine (A) and cytosine (C) residues, but remains inert toward base-paired A and C engaged in Watson-Crick interactions (Rouskin et al., 2014). Using this methodology, we identify stable stem-loop structure (SL3) positioned within SF3A3 5'UTR. To further validate the functional importance of SL3, the structural point mutant (SF3A3 5'UTR mut: A55C and U95A) and rescue (SF3A3 5'UTR res: A55C and U95A and rescuing point mutations G61U and U100G) sequences of SF3A3 5'UTR were cloned into the reporter plasmid. For the validation of these mutate-and-rescue constructs, plasmids were in vitro transcribed and either used directly (samples described as 'in vitro') for DMS-MaP-Seq probing.

2021-03-25 | GSE147504 | GEO

4U-DMS-MaP probing of nascent ribosomes

Project description:4U-DMS-MaP probing of nascent ribosomes

| PRJNA659772 | ENA

Targeted DMS probing of SF3A3 5' UTR

Project description:Targeted DMS probing of SF3A3 5' UTR

| PRJNA615008 | ENA

SHAPE and DMS probing of SLNCR1 lncRNA conserved region 403-780

Project description:The goal of this study was to understand the underlying structure of nucleotides 403-780 of the lncRNA SLNCR1, in-cell and when extracted from nuclear and cytoplasmic fractions. SHAPE and DMS probing revealed that the region is largely unstructured inside and outside of the cell, and appears protein-bound in primary melanoma cells.

2019-11-07 | GSE140048 | GEO

MeRIP sequencing analysis of BJAB cell line infected with EBV

Project description:MeRIP sequencing analysis of BJAB cell line infected with EBV

| PRJNA553159 | ENA

Gene expression patterns of EBV negative BJAB B-lymphoma lines stably and conditionally expressing EBNA-1

Project description:EBNA-1 is expressed in all EBV-associated malignancies and may play a role in transcription regulation through its DNA binding ability. This is our attempt to examine the effect of EBNA-1 on the expression of cellular genes. We have compared the transcription profiles of conditional and stable EBNA-1 transfected sublines of the EBV negative B-cell lymphoma BJAB where EBNA-1 was expressed for few days, few months or years. The non-specific effects were accounted by comparing the gene expression profiles of untransfected cells or cells transfected with the empty vector or cultured in the presence or absence of doxycycline.

2010-07-17 | GSE22964 | GEO

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