Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell RNA sequencing analysis of in vitro DENV1 infected cells

ABSTRACT: CEM.NKR.DC-SIGN cells were infected in vitro with DENV1 (strain WestPac74) for 18 hours, after which either total viable cells or viable cells expressing surface DENV1 NS1 were isolated by flow cytometric sorting. Sorted cells were processed for scRNAseq analysis using either a standard Oligo(dT) primer, or an Oligo(dT) primer supplemented with a DENV-specific RT primer

ORGANISM(S): Homo sapiens Dengue virus 1 Nauru/West Pac/1974

PROVIDER: GSE147103 | GEO | 2020/05/17

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Analysis of cell-associated DENV RNA by oligo(dT) primed 5' capture scRNAseq

Project description:Analysis of cell-associated DENV RNA by oligo(dT) primed 5' capture scRNAseq

| PRJNA613041 | ENA

Dengue Virus NS1 Replicon - Dengue virus (DENV) is a major human pathogen that belongs to the flavivirus genus

Project description:Dengue virus (DENV) is a major human pathogen that belongs to the flavivirus genus. Among non-structural viral proteins, NS1 is an enigmatic factor that is exclusively encoded by members of the flavivirus genus within the Flaviviridae family and accomplishes different functions during DENV infection. To gain insight into the molecular and cellular function of NS1 in viral replication, we generated a tagged NS1 DENV replicon and identified the associated host proteins during active viral replication. Replicons are self-replicating flavivirus RNAs containing large in-frame deletions in the structural genes and are useful tools to study translation and RNA amplification of several flaviviruses. To establish a global map of NS1-host protein interactions occurring during DENV replication, we stably expressed a DENV2 replicon encoding NS1 tagged with N-terminal FLAG and HA epitopes (FH-NS1) or the untagged version (WT) in three different human cell lines (Raji, HeLa and HAP1). Interactors of NS1 were identified by AP-MS/MS from these three different cell lines.

2017-11-29 | PXD008120 | Pride

Unified Feature Association Networks through Integration of Transcriptomic and Proteomic Data

Project description:Proteomic data from dengue virus infected U-937 cells. PVD_C samples were infected via antibody-mediated or DC-SIGN receptor mediated entry routes with wild-type DENV-4 or mock inoculum; time points 2, 8, 16, and 24 hours; 5 biological replicates. PVD_L samples were infected via antibody-mediated or DC-SIGN receptor mediated entry routes with wild-type DENV-1 or mock inoculum; time points 2, 6, 10, 18, 24, and 30 hours; 5 biological replicates.

2019-08-22 | PXD014780 | Pride

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 4tU cordycepin treatment

Project description:mPAT approach using an anchored oligo-dT (TV12VN) primer to determine changes to 3'UTR length in yeast upon cordycepin treatment and new transcription using 4-thiouracil (4tU) labelling of RNA. This appears as a T to C conversion in sequencing reads.

2021-06-25 | GSE160993 | GEO

Neurospora crassa early sexual development with MTP priming

Project description:Multi-targeting priming (MTP) for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences. We demonstrated superior performance of two MTPs compared to oligo-dT microarray profling and RNA tag sequencing the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development. Priming with MTPs in addition to oligo-dT resulted in higher sensitivity, a greater number of well-measured genes, more genes significantly differentially expressed, and a greater power to detect meager differences. Neurospora crassa mat A FGSC#2489 Three developmental stages and two different primers used for reverse transcription: mycelium oligo(dT) M1 protoperithecia oligo(dT) PP1 perithecia oligo(dT) PT1 mycelium oligo(dT)+ Multi-Targeted Primer [MTP] (M2) protoperithecia oligo(dT)+ MTP (PP2) perithecia oligo(dT)+ MTP (PT2)

2010-07-03 | E-GEOD-22658 | biostudies-arrayexpress

RNA-seq from sorted population of CD8 T cells (50 cells per sample) of human CD8 T memory stem cells (Tscm) subsets defined by surface expression of CD122 or CXCR3

Project description:Although it is recognised that CD8+ T memory stem cells (Tscm) are heterogeneous in phenotype and function, very few studies have sought to systematically examine these characteristics, particularly in human samples, as the population as a whole is rare and antigen-specific cells even more so. For each T cell subsets investigated, we have performed optimized RNAseq for small number of cells by adapting the Smartseq2 protocol from scRNAseq. The mini-bulk number of cells was chosen to reduce heterogeneity but also maintain an adequate transcriptomics signal. Adapted from Smartseq2 protocol from scRNAseq described by Picelli et al, cell lysis buffer was prepared by adding 1 μl RNase inhibitor (Clontech, Mountain View, USA) to 19 μl Triton X‐100 solution (0.2% v/v). CD8 T cell subpopulations (TN, TSCM, TCM and TEM together with TSCM CXCR3hi/lo and CD122hi/lo) were bulk sorted (50 cells/sample, with replicates) directly into 96-well PCR plates containing 2 μl lysis buffer, 1 μl dNTP mix (10 mM) and 1 μl oligo‐dT primer at 5 μM. Plates were stored at -80 °C until ready to perform the assay. Reverse-transcription and PCR amplifications were performed as described, with the exception of reducing the IS PCR primer to a 50 nM final concentration and increasing the number of cycles to 28. Sequencing libraries were prepared using the Nextera XT Library Preparation Kit (Illumina; San Diego, USA) and sequencing was performed on Illumina NextSeq500 sequencing platforms with 2×150bp paired-end read output, the read depth was approximately 1.3 million reads per sample.

2022-03-10 | E-MTAB-10208 | biostudies-arrayexpress

Saccharomyces cerevisiae grown in nitrogen depletion with oligodT priming

Project description:Multi-targeting priming (MTP) for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences. We demonstrated superior performance of two MTPs compared to oligo-dT microarray profling and RNA tag sequencing the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development. Priming with MTPs in addition to oligo-dT resulted in higher sensitivity, a greater number of well-measured genes, more genes significantly differentially expressed, and a greater power to detect meager differences. Saccharomyces cerevisiae S288c was grown on two different media and two different primers were used for reverse transcription: oligo(dT) and Multi-Targeted Primer [MTP] protoperithecia oligo(dT)+ MTP (PP2) perithecia oligo(dT)+ MTP (PT2). Two biological replicates and dye swapping

2010-07-20 | E-GEOD-22992 | biostudies-arrayexpress

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 4tU cordycepin treatment with rpb1 slow mutant

Project description:mPAT approach using an anchored oligo-dT (TV12VN) primer to determine changes to 3'UTR length in yeast with a slow RNA polymerase II mutant rpb1-1, complemented with wild-type RPB1 or a slow rpb1 mutant plasmid, upon cordycepin treatment and new transcription using 4-thiouracil (4tU) labelling of RNA. This appears as a T to C conversion in sequencing reads.

2021-06-25 | GSE160994 | GEO

Interactome of DENV2 NS1 and NS5 in Aedes albopictus mosquito cells

Project description:Efficient virus replication in its vector, Aedes mosquitoes, is essential for the transmission of arboviral diseases like dengue virus (DENV) in populations. In order to identify RNA-independent host factors involved in DENV replication in mosquitoes, we established a system expressing all non-structural proteins within the context of the macro protein complex as observed during viral infections. Mosquito host factors interacting with 3xFLAGED-tagged DENV non-structural proteins NS1 or NS5 proteins were identified by label-free mass spectrometry.

2022-08-25 | PXD031112 | Pride

Transcriptome Analysis of the Zebrafish Mind Bomb Mutant

Project description:To identify the genes differentially expressed in the zebrafish mibta52b mutant, genome-wide transcriptome analysis was performed using Serial Analysis of Gene Expression (SAGE). 335 transcripts were identified whose expressions were significantly altered in the mibta52b mutant as compared with the wild-type. After mRNA isolation using oligo(dT)25 beads (Dynal Biotech ASA, Oslo, Norway), cDNA synthesis was carried out using anchored oligo(dT) primers to reduce truncated cDNA through internal poly(A) priming (Nam et al., 2002). SAGE analysis was carried out as described (Velculescu et al., 1995) but was modified slightly according to Lee et al (Lee et al., 2007). We performed a low-cycle PCR (14 cycles) using the GeneAmp PCR System 2400 (Applied Biosystem, Foster City, CA) to amplify 3’cDNA in order to generate a sufficient amount of templates for SAGE analysis. The sense primer used was a SAGE primer 1 (5’-GGA TTT GCT GGT GCA GTA CA-3’) or SAGE primer 2 (5’-CTG CTC GAA TTC AAG CTT CT-3’); the antisense primer used was 5’-biotin- ACT ATC TAG AGC GGC CGC TT-3’, which was located in the 3’ end of all cDNAs generated from the anchored oligo(dT) primers. BsmFI-released fragments containing SAGE tags, were gel purified before being used for ditag formation and concatenation to provide high-quality tags for SAGE analysis. SAGE tag sequences were collected with Big-Dye sequencing and an ABI3730 sequencer, and tag sequences were extracted with SAGE 300 software. A total of 92,970 SAGE tags were collected from the two libraries.

2008-10-08 | E-GEOD-13050 | biostudies-arrayexpress

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