Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-Seq to investigate the role of membrane-to-cortex-attachment in mESc pluripotency

ABSTRACT: RNA-Seq dataset of mES cells to assess their pluripotency state and differentiation capability upon expression of endogenous (CAEzrin) or synthetic (iMC-linker) MCA-Proteins. Data were collected with 3 - 4 biological replicates per condition.

ORGANISM(S): Mus musculus

SUBMITTER: Charles Girardot

PROVIDER: E-MTAB-9404 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of wine yeast strains, parental and adaptively evolved for selective increase in aroma compounds originating in branched-chain or aromatic amino acid pathway

Project description:Adaptive laboratory evolution is highly effective for improving desired traits through natural selection. However, its applicability is inherently constrained to growth-correlated traits precluding traits of interest that incur a fitness cost, such as metabolite secretion. Here, we introduce the concept of tacking trait enabling natural selection of fitness-costly metabolic traits. The concept is inspired from the tacking maneuver used in sailing for traversing upwind. We use first-principle metabolic models to design an evolution niche wherein the tacking trait and fitness become correlated. Adaptive evolution in this niche, when followed by the reversal to the original niche, manifests in the improvement of the desired trait due to biochemical coupling between the tacking and the desired trait. We experimentally demonstrated this strategy, termed EvolveX, by evolving wine yeasts for increased aroma production. RNA-sequencing was performed for parental and evolved strains in the respective evolution niche and in natural grape must.

2021-12-30 | E-MTAB-10019 | biostudies-arrayexpress

RNAseq of HCT116 p53KO cells transfected with either siRNA silencing ZNF84 or with negative control siRNA, in 2 variants of experiment a) with doxorubicin treatment (doxorubicin added 48h post-transfection, for the next 48h before harvesting) b) untreated, cultured 72h post-transfection

Project description:The aim of this experiments was to characterise the transcriptomic changes occurring in cancer cells, in which ZNF84 gene is silenced, in control conditions and when cells undergo stress by being treated with cytostatic doses of doxorubicin. We anticipated that ZNF84 regulates the level of p21 cell cycle inhibitor and therefore contributes to senescence induction in response to stress. We wanted to know whether attenuation of senescence in cells with downregulated ZNF84 is accompanied by alterations in other biological processes and signalling pathways. Cells were transfected with 30 nM siRNA (against ZNF84 or negative control siRNA) and then either a) doxorubicin was added (48 hours after transfection and cells were cultured in the presence of the drug for another 48 hours) b) no drug was added (cells were cultured in drug-free medium for 72 hours post- transfection) Variants a) and b) were separate RNA sequencing experiments.

2021-05-05 | E-MTAB-9848 | biostudies-arrayexpress

RNA-seq of liver stage-derived parasites from wild-type and TCRδ-/- mice

Project description:P. berghei ANKA parasites were collected from the blood at 74h after infection of wild-type and TCRδ-/- mice with 2x10^4 sporozoites (samples were pooled from 3 mice/ group) and mRNA was sequenced by RNA-seq.

2019-04-11 | E-MTAB-6493 | biostudies-arrayexpress

RNA-seq to investigate YBX3 siRNA knockdown in HeLa cells

Project description:This study identifies the transcriptomic effects of YBX3 depletion after 2 days of siRNA knockdown. Unspecific siRNA and untreated cells were used as controls. The cells were grown in SILAC media and the effects on protein levels were measured by mass spectrometry. Also an eCLIP (E-MTAB-5888) experiment was performed to identify RNA targets of YBX3.

2019-05-10 | E-MTAB-7455 | biostudies-arrayexpress

Comparison of Trail+/+ versus Trail-/- splenic NK cells from naïve and LCMV-infected mice

Project description:Investigation of the change of the Trail-dependent NK cell transcriptome during short-term (24h) infection with lymphocytic choriomeningitis virus (LCMV). RNA sequencing-based transcriptomics analysis was performed in spleen-isolated (NK1.1+CD3-) NK cells from 3 naïve Trail+/+ mice, 3 naive Trail-/- mice, 4 LCMV-infected Trail+/+ mice, and 4 LCMV-infected Trail-/- mice.

2019-08-27 | E-MTAB-7562 | biostudies-arrayexpress

RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production.

Project description:Model-guided chassis strain design has the potential to accelerate cellfactory development. In this experiment genetic targets were identified in silico and implemented in vivo to design a yeast chassis strain for enhanced production of succinic, malic and fumaric acid. The phenotype of engineered chassis strains was further optimised through adaptive laboratory evolution. RNA-seq analysis of engineered yeast chassis strains, evolved strains and wild-type (CEN.PK background)was performed to determine the effect of engineered gene deletions and evolution on the transcriptome.

2021-07-01 | E-MTAB-9499 | biostudies-arrayexpress

RNA-seq comparing WT to HDAC3 knock-out clones in naïve mESCs, as well as SL and EpiLC differentiation conditions at two distinct time points (1 and 2 days)

Project description:Determine the transcriptomic effects that are associated with the distinct differentiation phenotypes of HDAC3 knock-out vs wildtype mESCs.<br>This experiment is part of the study: "Mechanistic framework of lineage restriction in embryonic stem cells" by Olivieri et al.

2021-03-14 | E-MTAB-9446 | biostudies-arrayexpress

RNA-seq for wild-type and Zbtb2 knock-out clones of mESCs in 2iLIF, EpiLC and SerumLIF conditions.

Project description:Zbtb2 mutant mouse embryonic stem cells are defective in exiting the pluripotent state. To determine the transcriptional changes underlying this phenotype we performed RNA-seq of wildtype and Zbtb2 mutant cells; in the naïve pluripotent state in 2iLIF, and after 24h and 48h of exposure to SerumLIF and epiblast-like cell (EpiLC) differentiation conditions.

2021-07-07 | E-MTAB-9797 | biostudies-arrayexpress

RNA-seq comparing WT to HDAC3 and Dax1 knock-out clones in cell-sorted populations in 2iLIF and SL(RA) differentiation conditions

Project description:In order to determine the transcriptomic profiles of PrE-induced cells following HDAC3 or Dax1 knock-out in SL(RA) differentiation conditions, RNA-seq was performed on Gata6+ or Nanog+ sort-selected cells. Profiles are contrasted with WT cells in the same differentiation conditions as well as to mock-sorted populations of the three genotypes in 2iLIF conditions.

2021-03-15 | E-MTAB-10150 | biostudies-arrayexpress

RNA-seq comparing WT to Dax1, Nr5a2 and Dax1/Nr5a2 knock-out clones in 2iLIF and SL differentiation conditions

Project description:Determine the transcriptomic effects that are associated with the knock-out of the inhibitor of PrE trans-differentiation Dax1 and the associated nuclear receptor Nr5a2.<br>This experiment is part of the study: "Mechanistic framework of lineage restriction in embryonic stem cells" by Olivieri et al.

2021-03-15 | E-MTAB-9447 | 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