Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of cytoplasmic and nucleoplasmic samples of a time-course of Ad5-infected A549 cells

ABSTRACT: RNA-seq of cytoplasmic and nucleoplasmic samples of a time-course of Ad5-infected A549 cells

PROVIDER: PRJEB57806 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR10509600_1.fastq.gz	Fastqsanger.gz
	ERR10509600_2.fastq.gz	Fastqsanger.gz
	ERR10509601_1.fastq.gz	Fastqsanger.gz
	ERR10509601_2.fastq.gz	Fastqsanger.gz
	ERR10509602_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 120

Similar Datasets

Analysis of cytoplasmic, nucleoplasmic, nucleolar transcriptome in Raw264.7 macrophages during LPS stimulation

Project description:To understand a novel function of nucleolus during infectious conditions, we purified cytoplasmic, nucleoplasmic, and nucleolar fractions from macrophages for a time course of LPS stimulation and performed RNA-seq.

2020-10-13 | GSE159346 | GEO

RNA-seq of cytoplasmic and nucleoplasmic samples of a time-course of Ad5-infected A549 cells

Project description:Interested in how Adenovirus infection regulates temporal changes and differential export of viral and cellular mRNAs, we infected A549 cells with HAdV-C5 (H5pg4100) at 6, 12, 24 and 48 hours post-infection. Cells were infected with a MOI of 30 ffu and a non-infected (mock) sample was also included. After the infection period, cells were collected by trypsinization and fractionated to separate nucleus and cytoplasm with an NP-40 lysis buffer and RNA was extracted from each sample with TRIzol, followed by a column extraction using the RNeasy Plus Mini Kit. The cDNA libraries were made from mRNAs by first performing a poly(A) selection to the total RNA sample. The cDNA libraries were generated with the ScriptSeq v2 RNAseq Kit using their strand-specific protocol and a multiplex-sequencing was performed on the HiSeq 2500 platform using a paired-end run with a depth of approximately 50 million reads per sample. Two biological replicates of each infection time point and cellular fraction were sequenced using three technical replicates.

2022-11-25 | E-MTAB-12386 | biostudies-arrayexpress

Analysis of cytoplasmic, nucleoplasmic, nucleolar transcriptome in Raw264.7 macrophages during LPS stimulation

Project description:Analysis of cytoplasmic, nucleoplasmic, nucleolar transcriptome in Raw264.7 macrophages during LPS stimulation

| PRJNA668397 | ENA

Gene expression profiles of human Ad5- and CMV-specific CD4 T cells

2014-08-07 | GSE60180 | GEO

Gene expression profiles of human Ad5- and CMV-specific CD4 T cells

Project description:Analysis of global gene expression profiles of FACS-sorted, human Ad5- and CMV-specific CD4 T cells from the same PBMC sample of healthy donros, using affymetrix Human Gene 2.0ST Gene-Chips; The analysis show that Ad5- and CMV-specific CD4 T cells demonstrate differential gene expression profiles even though the cells are from the same PBMC PBMC from healthy donors (n=3) were CFSE-labeled, then equally divided and stimulated with Ad5 and CMV antigens; On day 6 post stimulation, Ag-specific CD4 T cells were sorted by flow based on CFSE-low.

2014-08-07 | E-GEOD-60180 | biostudies-arrayexpress

Total nucleoplasmic RNA-seq in MCF-7

Project description:Deep sequencing of total RNA isolated from the nucleoplasmic fraction of MCF-7 cells.

2018-02-05 | GSE110149 | GEO

Gossypium darwinii isolate:AD5-18

Project description:Gossypium darwinii isolate:AD5-18 Genome sequencing

| PRJNA1045698 | ENA

Post-transcriptional Gene Silencing Mediated by microRNAs is Controlled by Nucleoplasmic Sfpq [Agilent]

Project description:There is a growing body of evidence about the presence and the activity of the miRISC in the nucleus of mammalian cells. Here, we show by quantitative proteomic analysis that Ago2 interacts with nucleoplasmic Sfpq in a RNA-dependent fashion. By HITS-CLIP and transcriptomic analyses, we demonstrated that Sfpq directly controls the miRNA targeting of a subset of crucial miRNA-target mRNAs when it binds locally. Sfpq modulates miRNA targeting in both nucleoplasm and cytoplasm, indicating a nucleoplasmic imprinting of Sfpq-target mRNAs that influence miRNA targeting in both cellular compartments. Mechanistically, Sfpq binds to a sizeable set of long 3’UTR forming long aggregates to optimize miRNA position/recruitment to selected binding sites, as we show for Lin28A mRNA. These results extend the miRNA-mediated post-transcriptional gene silencing into the nucleoplasm and indicate that an unique Sfpq-dependent post-transcriptional strategy for controlling both nuclear and cytoplasmic gene expression takes place in cells during physio-pathological events.

2017-10-20 | GSE89023 | GEO

Merck Ad5/HIV induces broad innate immune activation that predicts CD8+ T-cell responses but is attenuated by preexisting Ad5 immunity.

Project description:This SuperSeries is composed of the following subset Series: GSE22768: Systems analysis of the Merck Ad5/HIV vaccine reveals robust induction of a core innate immune gene network: in vivo analysis GSE22769: Systems analysis of the Merck Ad5/HIV vaccine reveals robust induction of a core innate immune gene network: in vitro analysis To better understand how innate immune responses to vaccination can lead to lasting protective immunity, we used a systems approach to define immune signatures in humans over 1 wk following MRKAd5/HIV vaccination that predicted subsequent HIV-specific T-cell responses. Within 24 h, striking increases in peripheral blood mononuclear cell gene expression associated with inflammation, IFN response, and myeloid cell trafficking occurred, and lymphocyte-specific transcripts decreased. These alterations were corroborated by marked serum inflammatory cytokine elevations and egress of circulating lymphocytes. Responses of vaccinees with preexisting adenovirus serotype 5 (Ad5) neutralizing antibodies were strongly attenuated, suggesting that enhanced HIV acquisition in Ad5-seropositive subgroups in the Step Study may relate to the lack of appropriate innate activation rather than to increased systemic immune activation. Importantly, patterns of chemoattractant cytokine responses at 24 h and alterations in 209 peripheral blood mononuclear cell transcripts at 72 h were predictive of subsequent induction and magnitude of HIV-specific CD8(+) T-cell responses. This systems approach provides a framework to compare innate responses induced by vectors, as shown here by contrasting the more rapid, robust response to MRKAd5/HIV with that to yellow fever vaccine. When applied iteratively, the findings may permit selection of HIV vaccine candidates eliciting innate immune response profiles more likely to drive HIV protective immunity. Refer to individual Series

2012-11-20 | E-GEOD-22822 | biostudies-arrayexpress