Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dual RNA-seq of diverse human, mouse and pig cell-types infected with various Salmonella strains

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): mixed sample: human cell line AGS and Salmonella Typhimurium SL1344

SUBMITTER: Konrad FÃ¶rstner

PROVIDER: E-GEOD-60144 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Dual RNA-seq â sRNA profiling in various cell types

Project description:Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little understood due to a paucity of macroscopic phenotypes in standard virulence assays. Here, we use a novel Dual RNA-seq approach for a single-step simultaneous RNA profiling in both pathogen and host to reveal molecular phenotypes of sRNAs during infection with Salmonella Typhimurium. We identify a new PhoP/Q-activated small RNA which upon bacterial internalization acts to temporally control the expression of both, invasion-associated effectors and virulence genes required for intracellular survival. This riboregulatory activity is shown to adjust the human response to replicating Salmonella, and have a pervasive impact on host RNA expression both inside and outside protein-coding regions including infection-specific alterations of an array of long noncoding RNAs. Our study provides a paradigm for a comprehensive RNA-based analysis of intracellular bacterial pathogens without their physical purification from a host and a new discovery route for hidden functions of pathogen genes. sRNA profiling in various cell types

2015-12-11 | E-GEOD-67947 | biostudies-arrayexpress

Dual RNA-seq â Comparative RNA-seq (in vitro medium shift experiment)

2015-12-11 | E-GEOD-67949 | biostudies-arrayexpress

Myogeneic differentiation in Rb1 or Kdm5a/Jarid1a/Rbp2 deficient mouse embryonic fibroblasts.

Project description:Cells lacking Rb1 are deficient in differentiation. Loss of Kdm5a rescues myogenic differentiation, as judged by appearance of morphologically normal myotubes that display expression of late markers of differentiation. In order to better understand how Kdm5a loss rescues differentiation, we induced mouse embryonic fibroblasts (MEFs) of different genotypes to undergo myogenic differentiation and analyzed gene expression changes in wild-type, Kdm5a-/-, Rb1-/- and Kdm5a-/-; Rb1-/- cells. Rb1-/- cells stained single nucleated, did not exhibit morphological changes and increased expression of the myogenic marker MYHC. Except for Rb1-/- cells, all other cells were undergoing successful convertion into aligned multinucleated myotubes and were MYHC-positive. We obtained purified populations of myotubes for the wild-type and Kdm5a-/-; Rb1-/- cells. RNA-seq analysis of gene expression in Rb1 or Kdm5a deficient MEFs that were induced for myogenic differentiation.

2015-08-12 | E-GEOD-53528 | biostudies-arrayexpress

Massively parallel reporter assays (MPRAs) of 175bp human genomic fragments containing variants in high LD with lead variants from obesity GWAS associations.

Project description:We performed a massively parallel reporter assay on 2,396 genomic regions containing single nucleotide polymorphisms that are in high linkage disequilibrium with 97 lead variants from an obesity GWAS (PMID: 25673413). Regions were transfected into human SGBS preadipocytes, SGBS mature adipocytes, 3T3-L1 preadipocytes, HT22 hippocampal cells, and GT1-7 cells and assessed for enhancer activity. The processed file contains the MPRA barcodes.

2021-05-22 | E-MTAB-10463 | biostudies-arrayexpress

syangArray

Project description:Gene expression was studied in the presence or absence of Otx2 (RNAi) in the Rex1GFPd2 mouse embryonic stem cell line (parental line; E14Tg2a) in undifferentiated and differentiated states.

2014-06-24 | E-MTAB-2239 | biostudies-arrayexpress

Massively Parallel Reporter Assay (MPRA) of 175 bp human genomic fragments containing variants in high LD with lead variants from asthma GWAS.

Project description:We performed a massively parallel reporter assay (MPRA) of 2,034 genomic regions containing single nucleotide polymorphisms (4,587 regions tested with 96,328 barcodes) that are in high linkage disequilibrium with lead variants from an asthma GWAS (PMID: 31036433). Test sequences were transfected into 16HBE14o- Human Bronchial Epithelial Cells, and assessed for enhancer activity by comparing RNA counts to DNA input counts. The processed files contain the MPRA barcodes, read counts and activities.

2025-03-11 | E-MTAB-14273 | biostudies-arrayexpress

Chromatin opening on CBFA2T3::GLIS2 iPSC-derived progenitors

Project description:Wild-type (CTRL) and CBFA2T3::GLIS2 induced pluripotent stem cell (iPSC) clones were differentiated into hematopoietic cells in vitro. Cells from day 13 in vitro differentiation were analysed. In addition, cells from CBFA2T3::GLIS2 iPSC were injected into immunodeficient murine recipients that developped leukemia with characteristics of patient leukemia. ATAC-seq was performed to characterize chromatin accessibility in cells from 3 conditions : - Control iPSC-derived hematopoietic cells in vitro (day 13 of differentiation) - CBFA2T3::GLIS2 iPSC-derived hematopoietic cells in vitro (day 13 of differentiation) - CBFA2T3::GLIS2 leukemic cells derived from the engraftment of day 13 CBFA2T3::GLIS2+ iPSC into immunodeficient murine recipients (in vivo).

2025-07-09 | E-MTAB-14204 | biostudies-arrayexpress

Parsing the interferon transcriptional network and its disease associations

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-11-24 | E-GEOD-75306 | biostudies-arrayexpress

syangRNAseq

2014-06-24 | E-MTAB-2245 | biostudies-arrayexpress

Tissue-specific changes in Tcrb conformation

Project description:We report the changes in Tcrb interactome upon transitioning from DN to DP stage of thymocyte development Examination of the interactomes of Eb and Trbv5 viewpoints in RAG-deficient DN and DP thymocytes

2015-07-08 | E-GEOD-68955 | 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