Mus musculus
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ABSTRACT:
PROVIDER: PRJNA125709 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We differentiated mouse embryonic stem (mES) cells spontaneously into embryoid bodies (EBs). Gene expression of biological replicates of undifferentiated ES cells (0-day), 4-day, 8-day and 14-day EBs were measured by Affymetrix microarrays. Keywords: time course
2010-02-25 | GSE12550 | GEO
Project description:ChIP on chip for H3K27me3 in murine ES cells comparing Undifferentiated and Day 3 differentiated. Paper Abstract: How polycomb group proteins repress gene expression in vivo is not known. Whilst histone modifying activities of the polycomb repressive complexes have been studied extensively, in vitro data has suggested a direct activity of the PRC1 complex in compacting chromatin. Here, we investigate higher-order chromatin compaction of polycomb targets in vivo. We show that polycomb repressive complexes are required to maintain a compact chromatin state at Hox loci in embryonic stem (ES) cells. There is specific decompaction in the absence of PRC2 or PRC1. This is due to PRC1, since decompaction occurs in Ring1B null cells that still have PRC2-mediated H3K27 methylation. Moreover, we show that the ability of Ring1B to restore a compact chromatin state, and to repress Hox gene expression in ES cells, is not dependent on its histone ubiquitination activity. We suggest that Ring1B-mediated chromatin compaction acts to directly limit transcription in vivo. Biological replicates: 3 independently grown, harvested, micrococcal nuclease digested and ChIP for H3K27me3. 6 Technical replicates.
2010-05-14 | E-GEOD-20201 | biostudies-arrayexpress
Project description:Affymetrix 430 2.0 mouse arrays were used for expression analyses in undifferentiated and differentiated PGK12.1 ES cells. We found that the X:autosome expression ratios calculated from the mean expression values of X-linked and autosomal genes from microarrays was ~1.4 in undifferentiated female ES cells and then decreased to 1.2 in PGK12.1 cells after 15-day embryoid body differentiation. Thus, a substantial level of X upregulation is already evident in these ES cells prior to differentiation. Our findings based on Affymetrix expression arrays are consistent with microarray analysis from other labs and our RNA-seq analysis of mouse female PGK12.1 ES cells. Mouse female ES cells PGK12.1 were differentiated by the EB (embryoid body) differentiation protocol. The presence of two active X chromosomes in undifferentiated female ES cells and one active X in 15-day differentiated cells was verified by Xist RNA FISH. Total RNA was prepared from undifferentiated and 15-day differentiated PGK12.1 and was used for expression array analyses to examine exprssion of the X chromosome during differentiation.
2013-02-15 | E-GEOD-44251 | biostudies-arrayexpress
Project description:ChIP on chip for H3K27me3 in murine ES cells comparing Undifferentiated and Day 3 differentiated. Paper Abstract: How polycomb group proteins repress gene expression in vivo is not known. Whilst histone modifying activities of the polycomb repressive complexes have been studied extensively, in vitro data has suggested a direct activity of the PRC1 complex in compacting chromatin. Here, we investigate higher-order chromatin compaction of polycomb targets in vivo. We show that polycomb repressive complexes are required to maintain a compact chromatin state at Hox loci in embryonic stem (ES) cells. There is specific decompaction in the absence of PRC2 or PRC1. This is due to PRC1, since decompaction occurs in Ring1B null cells that still have PRC2-mediated H3K27 methylation. Moreover, we show that the ability of Ring1B to restore a compact chromatin state, and to repress Hox gene expression in ES cells, is not dependent on its histone ubiquitination activity. We suggest that Ring1B-mediated chromatin compaction acts to directly limit transcription in vivo.
2010-05-14 | GSE20201 | GEO
Project description:Purpose: To compare gene expressions of undifferentiated cells and differentiated cells treated with basal media, basal media + FGF2, basal media + SU5402 and bsal media + ERKiII. Methods:For differentiation, hPSCs was set up 2 days before initiation of DE at Day 0 (D0). On D0, media was replaced with using RPMI/2%B27, Activin, CHIR99021, LY294002 +/- FGF2, SU5402 or TCS ERKi. The cells were harvested on D3. Cells were cultured in triplicates for each condition, total RNA extraction was performed and 1000 ng of purified RNA was sent for RNA-seq. Genes that are differentially expressed were analyzed by comparing RNA expression at different conditions. Results: Principal component analysis confirmed that our replicate samples clustered together, indicating good reproducibility. ACLY and ACLYF30 samples clustered close to each other but were non-overlapping, suggesting hish similarity in their cellular identities. Contrastingly, ACLYSU and ACLYERKi samples are found isolated from each other and also from undifferentiated hPSCs (UD), ACLY and ACLYF30 samples, indicating that the inhibition of FGFR or ERK1/2 had a huge impact on redirecting DE cell fate despite the presence of DE-inducing conditions. Conclusions: Blocking of FGFR with SU5402 and ERK2 signalling with ERKiII perturb cell cycle and cell fate specification even in the presence of definitive endoderm-inducing conditions.
2023-06-15 | GSE110806 | GEO
Project description:Affymetrix 430 2.0 mouse arrays were used for expression analyses in undifferentiated and differentiated PGK12.1 ES cells. We found that the X:autosome expression ratios calculated from the mean expression values of X-linked and autosomal genes from microarrays was ~1.4 in undifferentiated female ES cells and then decreased to 1.2 in PGK12.1 cells after 15-day embryoid body differentiation. Thus, a substantial level of X upregulation is already evident in these ES cells prior to differentiation. Our findings based on Affymetrix expression arrays are consistent with microarray analysis from other labs and our RNA-seq analysis of mouse female PGK12.1 ES cells.
2013-02-15 | GSE44251 | GEO
Project description:Expression data from undifferentiated and differentiated human ES cells
| PRJNA306784 | ENA
Project description:We differentiated mouse embryonic stem (mES) cells spontaneously into embryoid bodies (EBs). Gene expression of biological replicates of undifferentiated ES cells (0-day), 4-day, 8-day and 14-day EBs were measured by Affymetrix microarrays. Keywords: time course Mouse embroynic stem cells were spontaneously into EBs. The gene expression was measured on undifferentiated mES cells on gelatin (0-day), undifferentiated mES cells sorted by FACS on Oct4 GFP-day (0-day), 4-day, 8-day and 14-day EBs.
2010-03-09 | E-GEOD-12550 | biostudies-arrayexpress
Project description:Murine ES cells were grown on confluent OP-9 and differentiated along the hematopoitic lineage. To assess the effects of Notch in hematopoiesis, activated Notch was overexpressed from Day 5 to Day 8.
2011-04-03 | GSE28338 | GEO
Project description:All data are derived from the same batch of human ES cells (line H9, WA-09). With the exception of the “UD” file all files represent neural cell types derived from the undifferentiated hESCs. Following mechanical isolation, rosettes were maintained for various passages in the presence of defined growth factors and morphogen factors as indicated below at the R-NSC stage. Cells at the NSCFGF/EGF stage were derived from mechanically isolated neural rosettes that were purified and long-term expanded as attached monolayer cultures in serum free medium in the presence of FGF2/EGF. Keywords: differentiation of human ES cells (line H9, WA-09).
2008-02-15 | GSE9921 | GEO