Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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)

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

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Panagiotis Papasaikas

PROVIDER: E-MTAB-9446 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

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 for wild-type, Zbtb2, Zfp369 and Ubn2 knock-out clones of mESCs in 2iLIF and SerumLif differentiation conditions.

Project description:Zbtb2 binds to Zfp639 and Ubn2. To determine if these mediate Zbtb2’s transcriptional function we performed RNA-seq of wildtype, Zbtb2, Zfp639 and Ubn2 mutant cells; in the naïve pluripotent state in 2iLIF, and after 48h of exposure to SerumLIF.

2021-07-07 | E-MTAB-9798 | biostudies-arrayexpress

ATACseq of TNG-A derived mESCs comparing WT to Dax1, Nr5a2 and Dax1/Nr5a2 knock-out clones

Project description:ATACseq in WT, Dax1, Nr5a2 and Dax1/Nr5a2 knock-out clones of mESCs in order to determine the role of the Dax1/Nr5a2 complex on chromatin accessibility and the activity of cis-regulatory elements during differentiation.<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-9453 | biostudies-arrayexpress

Single-cell RNA-seq comparing WT, HDAC3 and Dax1 knock-out clones in SL(RA) differentiation conditions

Project description:We performed single-cell RNA-seq in order to characterize in high resolution the transcriptomic profiles, differentiation fates and heterogeneity of wild-type, HDAC3 or Dax1 knock-out cells in SL(RA) differentiation conditions.

2021-03-15 | E-MTAB-10147 | 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

ChIPseq for histone marks in WT and Hdac3 knock-out clones of TNG-A derived mESCs in 2iLIF and SL differentiation conditions

Project description:H3K27ac and H4K5ac ChIPseq in WT and Hdac3-/- mESCs in order to determine the role of Hdac3 on the activity of cis-regulatory elements during differentiation.<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-9450 | biostudies-arrayexpress

RNAseq of mll2wt and mll2[Y2602A] mESC and EpiLC

Project description:PolyA RNAseq of mouse ESCs and EpiLCs carrying a homozygous point mutation in the catalytic domain of mll2[Y2602A]. Total RNA was isolated from cell pellets using NEB Monarch Total RNA Miniprep Kit and libraries prepared using NEBNext RNA Ultra II kit (NEB E7770S, input: 350 ng of total RNA). Libraries were multiplexed and sequenced on a NextSeq500 (Paired-End; read length 40). Each sample is present in 3 biological replicates.

2023-11-15 | E-MTAB-13467 | biostudies-arrayexpress

Expression data from mouse ES cells after control RNAi (scramble siRNAs) or RNAi specific for Kdm6a treatment.

Project description:To address the functional role of KDM6A in the regulation of Rhox genes, male and female mouse ES cells were transfected with a mixture of three small interfering RNA duplexes, each of which targets a different region of Kdm6a mRNA. We found that Kdm6a knockdown in mouse ES cells caused a decrease in expression of a subset of Rhox genes, Rhox6 and 9. Furthermore, Rhox6 and 9 expression was decreased in female ES cells but not male ES cells indicating that KDM6A regulates Rhox gene expression in a sexually dimorphic manner. Mouse ES cells were treated by Invitrogen scramble siRNA duplexes or specific siRNA duplexes and used for RNA extraction and hybridization on Affymetrix microarrays. Four RNA samples from two independent double-RNAi treatments and two single-RNAi treatment in undifferentiated female ES cells PGK12.1, and RNA samples from two single-RNAi treatments in undifferentiated male ES cells WD44 were assayed for expression changes by arrays.

2013-03-13 | E-GEOD-45034 | biostudies-arrayexpress

Expression data from mouse ES cells after control RNAi (scramble siRNAs) or specific RNAi (siRNAs for specific genes) treatment

Project description:To address the functional role of MOF in mammalian X upregulation, male and female mouse ES cells were transfected with a mixture of three small interfering RNA duplexes, each of which targets a different region of Mof mRNA. We found that MOF knockdown in mouse ES cells caused a greater drop in expression of X-linked genes compared to autosomal genes, as measured by expression array analyses. The strongest effect was observed on medium-expressed X-linked genes. We next examined components of the two known MOF protein complexes, MSL1 (male-specific lethal1) and NSL1 (nonspecific lethal1). Knockdown of MSL1 but not NSL1 in undifferentiated female ES cells PGK12.1 specifically caused a decrease in expression levels of X-linked genes. Cells co-transfected with both MOF and MSL1 siRNAs had similar expression changes to MSL1 knockdown alone, indicating that these components probably operate within the same complex but are not additive. Our findings that key components of the MSL but not NSL complex play a role in upregulation of mammalian X-linked genes in ES cells. Mouse ES cells were treated by Invitrogen scramble siRNA duplexes or specific siRNA duplexes and used for RNA extraction and hybridization on Affymetrix microarrays. Six RNA samples from two independent double-RNAi treatments and one single-RNAi treatment in undifferentiated female ES cells PGK12.1, and RNA samples from two single-RNAi treatments in undifferentiated male ES cells WD44 or E14 were assayed for expression changes by arrays. RNA samples from three MSL1RNAi treatments, two MOF/MSL1RNAi treatments and three NSL1RNAi treatments in undifferentiated female ES cells PGK12.1 were assayed by arrays.

2013-02-15 | E-GEOD-44252 | 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