RNAseq in Dppa2 knockout or wildtype TX1072 ESC during and after Xist over-expression
Ontology highlight
ABSTRACT:
INSTRUMENT(S): NextSeq 500
ORGANISM(S): Mus musculus
SUBMITTER: Charles Girardot
PROVIDER: E-MTAB-11183 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Chromatin accessibility was assayed in wildtype or Dppa2 knockout ESC after 26 days of release of the trigger imposed by epigenetic editing. Samples were collected in two clonal knockout and wildtype lines after sorting at FACS of cells which maintained a repressive Esg1-tdTomato (TOMneg) reporter expression after 26 days of DOX washout (release of the trigger).
2021-11-23 | E-MTAB-10522 | biostudies-arrayexpress
Project description:JARID2 ChIP-seq profile mediated by Xist was investigated using two separate approaches: In the first approach, we use the TX1072 female embryonic stem cell (ESC) line; this is a genetically polymorphic ESC line derived from a mouse with one X-chromosome (X-chr) from the Mus musculus castaneus (Cast) origin and the other of Mus musculus domesticus, C57BL/6 (BL6) strain origin, containing an inducible promoter on the BL6 Xist allele; differentiation and simultaneous induction of Xist for 4 days results in the inactivation of ONLY the BL6-derived X-chr and coating by JARID2 protein. We analysed this ESC line in the undifferentiated state, in which both X-chrs are active (and not coated by JARID2), and also after 4 days of differentiation under Xist inducible conditions, in which cells display one inactive X-chr from BL6 origin and one Xa of the Cast origin; the presence of SNPs allows for the comparison of the degree and localisation of JARID2 enrichment on the inactive X-chr versus the active X-chr; our results suggests that JARID2 is enriched on the inactive X-chr chromosome-wide and not in confined peaks as elsewhere in the genome; This pattern resembles patterns of Xist enrichment published before (Engreitz et al., 2013). In the second approach, we use a male ESC line that carries an inducible Xist transgene (TG) on chromosome 11 (chr11) (Wutz et al., 2000) in the presence (36:11 WT) or the absence of Eed (36:11 Eed-/-) Induction of Xist TG results in Xist coating and enrichment of JARID2 across the chr11, regardless of the presence of Eed when assess by IF/Xist RNA FISH experiments. We compare inducible and uninducible condition in both the 36:11 WT and Eed-/- ESCs; this way, we could assess the Xist-mediated JARID2 recruitment and the effect of the absence of Eed-/-; Our results shows that Xist induction result in a chromosome-wide enrichment of JARID2 on chr11, in a manner that resembles enrichment on the inactive X-chr; this pattern seem to be independent of EED, showing that in contrast to other regions in the genome where JARID2 occupancy is abrogated in the absence of EED, Xist-mediated JARID2 recruitment is not affected. JARID2 ChIP-seq analysis in differentiating female ESCs (TX1072) and in a male ESC harbouring a Xist transgene on chromosome 11 in WT and Eed-/- genetics settings
2014-01-23 | E-GEOD-52073 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in Candida albicans WO-1 grown aerobically in xylose, compared to the same strain grown aerobically in glucose. A six array study using total RNA recovered from three separate cultures of Candida albicans WO-1 grown in glucose and three separate cultures of Candida albicans WO-1 grown in xylose. Each array measures the expression level of 373,067 probes (average probe length 55.2 +/- 4.0 nt) tiled across the Candida albicans WO-1 genome with a median spacing distance of 31 nt. During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.
2011-10-19 | E-GEOD-24857 | biostudies-arrayexpress
Project description:Enrichment of DPPA2 was assessed by CUT&RUN-sequencing in wildtype Esg1-tdTomato reporter mESC line.
2021-11-23 | E-MTAB-11182 | biostudies-arrayexpress
Project description:In vertebrates, the catalytic core of PRC1 comprises RING1A/B and one of six homologues of the Polycomb group RING finger (PCGF) protein. Unique characteristics of PCGF1-6 in turn define distinct subunit assemblies, broadly subdivided into canonical and non-canonical PRC1 complexes. This RNA-seq experiment aimed to test the hypothesis that Pcgf3/5 gene knockout abrogates Xist mediated gene repression. In this experiment, Pcgf3fl/flPcgf5-/- and Pcgf3-/-Pcgf5-/- mESCs bearing Xist transgene on chromosome 16 (clone C3F8) were cultured in differentiating conditions: plated on non-gelatinized TC dish in ES medium without LIF for 72 hours with (+dox) and without doxycycline. RNA was isolated from 4 biological replicates. In analysed cells chromosome 16 bears inducible Xist and the whole study investigates role of PCGF3 and PCGF5 in Xist-dependednt gene silencing, therefore both bam files containing alignments and counts per gene were uploaded to ArrayExpress only for chromosome 16. Genome-wide data can be provided upon request.
2018-04-04 | E-MTAB-5642 | biostudies-arrayexpress
Project description:The role of Xist-mediated Polycomb recruitment in the initiation of X-chromosome inactivation
2019-08-29 | PXD014287 | Pride
Project description:JARID2 ChIP-seq profile mediated by Xist was investigated using two separate approaches: In the first approach, we use the TX1072 female embryonic stem cell (ESC) line; this is a genetically polymorphic ESC line derived from a mouse with one X-chromosome (X-chr) from the Mus musculus castaneus (Cast) origin and the other of Mus musculus domesticus, C57BL/6 (BL6) strain origin, containing an inducible promoter on the BL6 Xist allele; differentiation and simultaneous induction of Xist for 4 days results in the inactivation of ONLY the BL6-derived X-chr and coating by JARID2 protein. We analysed this ESC line in the undifferentiated state, in which both X-chrs are active (and not coated by JARID2), and also after 4 days of differentiation under Xist inducible conditions, in which cells display one inactive X-chr from BL6 origin and one Xa of the Cast origin; the presence of SNPs allows for the comparison of the degree and localisation of JARID2 enrichment on the inactive X-chr versus the active X-chr; our results suggests that JARID2 is enriched on the inactive X-chr chromosome-wide and not in confined peaks as elsewhere in the genome; This pattern resembles patterns of Xist enrichment published before (Engreitz et al., 2013). In the second approach, we use a male ESC line that carries an inducible Xist transgene (TG) on chromosome 11 (chr11) (Wutz et al., 2000) in the presence (36:11 WT) or the absence of Eed (36:11 Eed-/-) Induction of Xist TG results in Xist coating and enrichment of JARID2 across the chr11, regardless of the presence of Eed when assess by IF/Xist RNA FISH experiments. We compare inducible and uninducible condition in both the 36:11 WT and Eed-/- ESCs; this way, we could assess the Xist-mediated JARID2 recruitment and the effect of the absence of Eed-/-; Our results shows that Xist induction result in a chromosome-wide enrichment of JARID2 on chr11, in a manner that resembles enrichment on the inactive X-chr; this pattern seem to be independent of EED, showing that in contrast to other regions in the genome where JARID2 occupancy is abrogated in the absence of EED, Xist-mediated JARID2 recruitment is not affected.
2014-01-23 | GSE52073 | GEO
Project description:By comparing mouse fibroblasts from two parental strains (Bl6 and Spretus) with fibroblasts from their first generation offspring (F1) we can detect allele specific expression of proteins. The Bl6 and Spretus lines are evolutionary distant and harbour many SNPs in their genomes which when synonomous we can detect on the protein level using mass spectrometry. By mixing SILAC labeled Bl6, Spretus and F1 offspring cell lines we can detect peptides shared between all three cell lines and also SNP peptides that are only expressed in the F1 cells and either Bl6 or Spretus cells. By comparing the abundance of the shared peptides and the SNP peptides we can quantify how much of a protein in the F1 cells that comes from the paternal or maternal allele. This data were then further compared to polysome profiling data. Azidohomoalanine labeling was used to enrich newly synthesized proteins from the three cell lines.
2015-08-18 | PXD002337 | Pride
Project description:The effect of the GSK3 inhibitor Azakenpaullone (Azak) and the differentiation agent retinoic acid (RA) was studied in low and high MYCN levels in the MYCN inducible neuroblastoma cell line SH-SY5Y/6TR(EU)/pTrex-Dest-30/MYCN (SY5Y-MYCN). Azak was dissolved in DMSO in order to apply it to the cells. Therefore a vehicle control consisting of SY5Y-MYCN cells treated with 24h 1 ul/ml DMSO only was used in duplicates. Doxycycline (Sigma) dissolved in water was used at a final concentration of 1ug/ml to induce MYCN expression in SY5Y-MYCN. A co-treatment study with Dox and Azak was conducted. SY5Y-MYCN cells were treated with 24h Azak, 24h Azak & 48h Dox and 48h Dox, with biological duplicates. 1 uM RA (dissolved in DMSO) and 1 ug/mL Doxycycline were given individually and in combination. SY5Y-MYCN cells were treated with 24h RA, 24h RA & 48h Dox, and 48h Dox and RNA was extracted in biological duplicates. For the 24h RA & 48h Dox co-treatment cells were treated with Dox for 24h and then with RA and fresh Dox for a further 24h.
2015-06-30 | E-MTAB-2689 | biostudies-arrayexpress
Project description:A number of key regulators of mouse embryonic stem (ES) cell identity, including the transcription factor Nanog, show strong expression fluctuations at the single cell level. The molecular basis for these fluctuations is unknown. Here we used a genetic complementation strategy to investigate expression changes during transient periods of Nanog downregulation. Employing an integrated approach, that includes high-throughput single cell transcriptional profiling and mathematical modelling, we found that early molecular changes subsequent to Nanog loss are stochastic and reversible. However, analysis also revealed that Nanog loss severely compromises the self-sustaining feedback structure of the ES cell regulatory network. Consequently, these nascent changes soon become consolidated to committed fate decisions in the prolonged absence of Nanog. Consistent with this, we found that exogenous regulation of Nanog-dependent feedback control mechanisms produced more a homogeneous ES cell population. Taken together our results indicate that Nanog-dependent feedback loops play a role in controlling both ES cell fate decisions and population variability. Total of 30 samples, 10 conditions in triplicates; Cell samples were harvested at day0 (Dox present, Nanog expressing, NgR day0 +Dox), and at days 1,3 and 5 days after dox withdrawal (NgR day1 -Dox, NgR day3 -Dox and NgR day5 -Dox respectively). Additionally, at each time-point a set of samples was further treated with a twelve-hour pulse of dox before being harvested (NgR day1+ 12h Dox, NgR day3+12h Dox and NgR day5+12h Dox) and compared with untreated control samples harvested at the same time (NgR day1- 12h Dox, NgR day3-12h Dox and NgR day5-12h Dox) . All time points were performed in triplicates. We performed Affymetrix GeneChip® Mouse Gene 1.0 ST arrays analyses of mouse embryonic stem cell gene expression profiles at each time point. BD MacArthur and A Sevilla contributed equally to this study
2012-08-30 | E-GEOD-40335 | biostudies-arrayexpress