Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells

ABSTRACT: We developed a tunable ligation technology to alter beads used for to capture mRNA for single-cell RNA sequencing (e.g. Drop-seq); we call this technique droplet assisted RNA targeting by single cell sequencing, or DART-seq. In the study, we applied the new technology to capture viral genome transcripts of recombinant type 3 Dearing orthoreovirus infecting murine L929 cells. In addition to capture of targeted viral gene transcripts, we were also able to simultaneosly pull-down polyadenylated mRNA from the L929 cells to observe host-pathogen interactions. We also applied the technology to efficiently measure natively paired heavy and light chain amplicons from B lymphocyte cells in a collection of human peripheral blood mononuclear cells.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE113675 | GEO | 2018/04/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

In vitro study of role of Sigma B in pathogenesis of Avian Reovirus

Project description:Using microarray technology, we aim to identify in vitro host gene expression for understanding the crosstalk of signaling pathways that leads to the joint pathogenesis in Avian orthoreovirus infection.

2018-05-09 | GSE103067 | GEO

L929 vs L929IRF8 following 4hr IFNbeta treatment (1000U/ml)

Project description:Identify genes like Ifit1 which are induced in L929 cells but not L929 cells expressing ectopic IRF8

2016-04-30 | GSE75126 | GEO

Improved methods for deamination-based m6A detection

Project description:We present an improved version of DART-seq which utilizes a variant of the YTH domain engineered to achieve enhanced m6A recognition in APO1-YTH (D422N). In addition, we develop in vitro DART-seq and show that it performs similarly to cellular DART-seq and can map m6A in any sample of interest using nanogram amounts of total RNA.

2022-05-11 | GSE196416 | GEO

Effect of TNF-α on gene expression of L929 cells

Project description:To investigate the TNF-α in the regulation of L929 cells.We performed gene expression profiling analysis using data obtained from RNA-seq of L929 cells activated by TNF-α.

2022-05-09 | GSE202376 | GEO

Gene expression analysis of cells sensitive to necrosis (L929) and cells sensitive to apoptosis (NIH3T3).

Project description:To explore gene expression profiles of cells sensitive to necrosis (such as L929 cells) and those sensitive to apoptosis (such as NIH3T3 cells), we conducted expression microarray analysis of L929 cells and NIH3T3 cells.

2008-10-31 | GSE13335 | GEO

Evaluation of single cell classifiers for single cell RNA-seq datasets

Project description:Three human cell lines, K562, HEK293T and A431, and one murine cell line, L929, are mixed with equal proportion in two experiments. One mixture, named Mix3, consists of K562, HEK293T and L929. The other, named Mix4, consists of K562, HEK293T, A431 and L929. These cell lines were processed with the Singleron GEXSCOPETM protocol using GEXSCOPETM Single Cell RNA Library Kit (Singleron) and sequenced on an Illumina Xten. FASTQ data were preprocessed using fastp and STAR.

2019-11-27 | GSE128982 | GEO

Proteomics characterisation of the L929 cell supernatant and its role in BMDM differentiation

Project description:Bone marrow-derived macrophages (BMDMs) are a key model system for studying macrophage biology in vitro. Commonly used methods to differentiate macrophages from bone marrow are treatment with either recombinant M-CSF or the supernatant of L929 cells, which secrete M-CSF. However, little is known about the composition of L929 conditioned media (CM) and how it affects BMDM phenotype. Here, we used quantitative mass spectrometry to characterise the kinetics of protein secretion from L929 cells over a two-week period. While M-CSF is very abundant in L929 CM, we identified several other immune-regulatory proteins at surprisingly high abundance. L929 CM induced a slightly pre-activated phenotype and the expression of a number of known innate immune proteins in macrophages. This resource will be valuable to all researchers using L929 CM for the differentiation of BMDMs.

2021-04-13 | PXD021026 | Pride

Gene expression profiling in zebrafish embryos exposed to 3,4-dichloroaniline (3,4-DCA)

Project description:The zebrafish (Danio rerio) embryo toxicity test (DarT) is considered as an alternative to the acute fish toxicity test. However, DarT rarely reveals information on the mechanisms underlying a toxic effect and is relatively insensitive compared to chronic toxic effects. We hypothesized that, by using gene expression profiles as an additional endpoint, it may be possible to increase the sensitivity and predictive value of DarT. Therefore we exposed zebrafish embryos for 48 h to the reference compound 3,4-dichloroaniline and analyzed gene expression patterns with a 14 k oligonucleotide array. Keywords: differential gene expression upon chemical exposure in zebrafish embryos

2006-11-08 | GSE6228 | GEO

Transcription profiling of mouse D10.G4.1 T-cells treated with neuromedin U for different length of time to study the effect of neuromedin on gene expression in T cells.

Project description:Effects of Neuromedin-U on gene expression in mouse D10.G4.1 T-cells natively expressing the GPCR Axor13

2007-12-13 | E-GEOD-1791 | biostudies-arrayexpress

Incorporation of In Vitro Techniques for Botanicals Dietary Supplement Safety Assessment – Towards evaluation of Developmental and Reproductive Toxicity (DART)

Project description:As complex mixtures, botanicals present unique challenges when assessing safe use, particularly when endpoint gaps exist that cannot be fully resolved by existing toxicological literature. Obtaining data for developmental and reproductive toxicity (DART) can be particularly difficult as this is a frequent data gap for botanicals. Here we explore in vitro receptor binding and enzyme activity assays as well gene expression studies as alternative tools to inform on DART relevent modes of action. Botanicals suspected to have DART effects in addition to herbs with a significant history of use were tested at biologically relevant doses to probe activity at a molecular level. Additionally, gene expression changes in a number of different cell types were analysed using the connectivity mapping approach (CMap) to identify modes of action through a functional read across approach. Together, these two data streams increase the confidence in predictions of biological mode of action and inform potential DART risk by way of potency comparisons and/or a margin of internal exposure approach.

2020-05-01 | GSE144235 | 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