Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dynamic changes in gene expression during early differentiation of embryonic stem cells

ABSTRACT: We monitor the changes in genome-wide gene expression 6, 12 and 24 hours after removal of LIF and 2i from the ES cell culture media.

ORGANISM(S): Mus musculus

PROVIDER: GSE63831 | GEO | 2020/01/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells

2013-07-12 | GSE41923 | GEO

RNA-seq analysis of ES cell populations with different functional potentials in serum/LIF and 2i/LIF, as well as analysis of the transcriptional effect of LIF in ground state (2i) culture conditions.

Project description:We report that ES cells cultured in ground state (2i and 2i/LIF) culture conditions are heterogeneous and show heterogeneus expression of extraembryonic markers. Using a highly sensitive reporter for the endoderm marker Hex we can sort Hex high and low populations from either serum/LIF or 2i/LIF and demonstrate that they have different functional properties. Here we explored the transcriptional basis of these functional differences and noted that Hex low (HV-) and Hex high (HV+) populations showed more distinct expression profiles in 2i/LIF than in serum/LIF. Additionally in 2i/LIF the HV+ population showed an upregulation of extraembryonic markers (such as trophoblast stem cell specific genes) and also imprinted genes compared to the HV- population, which is not observed when these populations are sorted from serum/LIF. We also analysed the transcriptional effect of LIF in 2i by analysing unsorted ES cells cultured in either 2i alone or 2i with LIF. We observed that the addition of LIF led to an upregulation of extraembryonic markers but did not effect the expression of pluripotency genes, other than Klf4. Additionally, the most significantly upregulated genes from 2i/LIF cultured ES cells compared to 2i cultured ES cells showed the greatest correlation to placental tissue when compared to the GNF tissue specific expression database. This analysis, alongside functional experiments, suggested that HV+ ES cells in 2i/LIF corresponded to an extraembryonically primed population of cells and that the addition of LIF supported this population.

2013-06-11 | GSE45182 | GEO

Distinct DNA methylomes of 2i and serum mouse ES cells are interconvertible and reflect pre- and post-implantation embryonic states

Project description:This study describes the DNA methylation profiling using whole-genome bisulfite sequencing of mouse ES cells, either derived and maintained in 2i serum-free NDiff medium, or in the presence of serum and LIF, or maintained and derived in the presence of serum and LIF and subsequently adapted to 2i serum-free NDiff medium, or maintained and derived in the presence of 2i and LIF and subsequently adapted to 2i serum. DNA methylation profiling using whole-genome bisulfite sequencing of 14 samples, 3 different lines (E14, XT67E1, Rex/GFP-2i) of pluripotent mouse ES cells as well during conversion from 2i to serum and vice versa.

2013-07-12 | E-GEOD-41923 | biostudies-arrayexpress

Trim24 ChIP-seq in embryonic stem (ES) cells grown by 2i+LIF (2iL) and serum media

Project description:ChIP followed by next generation sequencing against Trim24 was performed in mouse embryonic stem (ES) grown either in 2i+LIF (2iL) or serum media. Two biological replicates for each condition were sequenced using Illumina HiSeq. Two input controls (no IP) were also generated for each condition.

2016-11-08 | E-MTAB-3802 | biostudies-arrayexpress

Expression profiling of mouse embryonic stem cells by mass spectrometry

Project description:Embryonic stem cells from B6 and NOD backgrounds were derived freshly in the presence of 2i. After 3-5 passages on feeders, ES cells were cultured in 2i media without any feeders for several passages. In order to identify differentially expressed genes and proteins, we performed RNA-Seq and mass spectromety analysis respectively. Among the differentially expressed genes, we identified several important players in innate and adaptive immunity. Several of these genes had been linked to onset of type-1 diabetes. Proteomics analysis was able to quantitative differences in protein expression among the B6 and NOD ES cell lines.

2020-08-31 | PXD020055 | Pride

RNA-seq analysis of ES cell populations with different functional potentials in serum/LIF and 2i/LIF, as well as analysis of the transcriptional effect of LIF in ground state (2i) culture conditions.

2013-06-11 | E-GEOD-45182 | biostudies-arrayexpress

Ground state of pluripotency cannot be maintained in mouse embryonic stem cells upon prolonged inhibition of GSK3

Project description:We compare gene expression changes in mESCs culture in serum/LIF or 2i/LIF which favour the ground state pluripotency. Published RNASeq data where compared with newly generated data set in order to indentify transciptional signatures associated with pluripotency of mouse ES cells

2019-03-03 | GSE70436 | GEO

RNA-seq on Hesx1+/+ and Hesx1-/- ES cells deprived of 2i/LIF for 24 hours

Project description:Hesx1+/+ and Hesx1-/- ES cells were cultured in 2i/LIF conditions for 5 passages, to induce a ground pluripotency state. Subsequently, inhibitors were removed to stimulate exit from ground pluripotency, and whole transcriptomics analysis was performed 24 hours after removal.

2018-05-21 | E-MTAB-5816 | biostudies-arrayexpress

Gain of chromatin loops marks the exit from naive pluripotency - ChIP seq for CTCF and Rad21

Project description:ChIP-seq to map the binding sites for CTCF and cohesin subunit Rad21 in the naive mES cells (46C cell line grown in the 2i/LIF condition) and in the neural stem cells (derived from the 46C ES cells using the mono-layer differentiation protocol, grown in the N2B27 medium these cells are Nestin+). The naive mES cells were grown in two different media (fetal bovine serum, FBS and 2i/LIF culture - naive pluripotency conditions) as detailed in the growth protocols.

2018-11-08 | E-MTAB-5732 | biostudies-arrayexpress

Trim24 ChIP-seq in embryonic stem (ES) cells grown by 2i+LIF (2iL) and serum media

Project description:Trim24 ChIP-seq in embryonic stem (ES) cells grown by 2i+LIF (2iL) and serum media

| PRJEB10107 | ENA