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TranscriptomicsRNA-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)
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.
ORGANISM(S): Mus musculus 
2021-03-14 | E-MTAB-9446 | biostudies-arrayexpress
TranscriptomicsRNA-seq comparing WT to Dax1, Nr5a2 and Dax1/Nr5a2 knock-out clones in 2iLIF and SL differentiation conditions
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.
This experiment is part of the study: "Mechanistic framework of lineage restriction in embryonic stem cells" by Olivieri et al.
ORGANISM(S): Mus musculus 
2021-03-15 | E-MTAB-9447 | biostudies-arrayexpress
TranscriptomicsChIPseq for histone marks in WT and Hdac3 knock-out clones of TNG-A derived mESCs in 2iLIF and SL differentiation conditions
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.
This experiment is part of the study: "Mechanistic framework of lineage restriction in embryonic stem cells" by Olivieri et al.
ORGANISM(S): Mus musculus 
2021-03-15 | E-MTAB-9450 | biostudies-arrayexpress
TranscriptomicsATACseq of TNG-A derived mESCs comparing WT to Dax1, Nr5a2 and Dax1/Nr5a2 knock-out clones
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.
This experiment is part of the study: "Mechanistic framework of lineage rest...
ORGANISM(S): Mus musculus 
2021-03-15 | E-MTAB-9453 | biostudies-arrayexpress
TranscriptomicsHigh throughput sequencing of Piwi bound piRNAs from Drosophila ovaries in which key factors for primary piRNA biogenesis in somatic support cells were knocked down using RNAi
In Drosophila, PIWI proteins and bound PIWI interacting RNAs (piRNAs) form the core of a small RNA mediated defense system against selfish genetic elements. Within germline cells piRNAs are processed from piRNA clusters and transposons to be loaded into Piwi/Aubergine/AGO3 and a subset of piRNAs und...
ORGANISM(S): Drosophila melanogaster 
2010-10-03 | E-GEOD-23560 | biostudies-arrayexpress
TranscriptomicsNovel piRNA Pathway Components Identified Among the Class of TUDOR Domain Containing Proteins
PIWI proteins and their bound piRNAs form the core of a gonad specific small RNA silencing pathway in animals that protects the genome against the deleterious activity of transposable elements. Recent studies linked the piRNA pathway to TUDOR biology, where TUDOR domains of various proteins recogniz...
ORGANISM(S): Drosophila melanogaster 
2011-08-16 | E-GEOD-30955 | biostudies-arrayexpress
TranscriptomicsRNA-seq comparing WT to HDAC3 and Dax1 knock-out clones in cell-sorted populations in 2iLIF and SL(RA) differentiation conditions
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 mo...
ORGANISM(S): Mus musculus 
2021-03-15 | E-MTAB-10150 | biostudies-arrayexpress
TranscriptomicsMajor concepts of piRNA biogenesis revealed by the analysis of Shutdown, a co-chaperone with essential roles in the biogenesis of all Drosophila piRNA populations
In animal gonads, 23-30nt long PIWI interacting RNAs (piRNAs) guarantee genome integrity by guiding the sequence specific silencing of selfish genetic elements such as transposons. Two major branches of piRNA biogenesis, namely primary processing and ping-pong amplification, feed into the PIWI clade...
ORGANISM(S): Drosophila melanogaster 
2012-06-29 | E-GEOD-38728 | biostudies-arrayexpress
ProteomicsThe interactome of Zbtb2 in mouse embryonic stem cells
Zbtb2 is a transcription factor that plays a role in mouse embryonic stem cell (mESC) differentiation. We pulled-down endogenously tagged Zbtb2-FLAG in mESCs and found a complex interactome. We characterized the Zbtb2 complex further by co-pull-downs of overexpressed Zbtb2-AVI, after mutation of ind...
ORGANISM(S): Mus musculus (Mouse) 
2021-07-14 | PXD025520 | Pride
Zbtb2 interactome Development Mouse embryonic stem cells 
ProteomicsThe interactomes of Ubn1 and Ubn2 in mouse embryonic stem cells
Ubn1 and Ubn2 are essential subunits of the Histone Regulator A (HiRA) complex, the H3.3 histone variant chaperone for euchromatin. We pulled-down Ubn1 and Ubn2 with a C-terminal AVI-tag in mouse embryonic stem cells and identified, besides all known components of the complex, transcription factors ...
ORGANISM(S): Mus musculus (Mouse) 
2021-07-14 | PXD025466 | Pride
Mus musculus Stem cel Cell culture l 
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