GEO DataSets

Analysis of lysine-specific demethylase 1 (Lsd1)-deficient trophoblast stem cells (TSCs) up to 4 days after the induction of differentiation. Lsd1 is an epigenetic regulator. Results provide insight into the role of Lsd1 in TCS differentiation.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation, 2 protocol, 3 time sets

Platform:

GPL1261

Series:

GSE38277

18 Samples

Download data: CEL

(Submitter supplied) Stem cells reside in specific niches providing stemness-maintaining environments. Thus, the regulated migration from these niches is associated with differentiation onset. However, mechanisms retaining stem cells in their niche remain poorly understood. Here, we show that the epigenetic regulator lysine-specific demethylase 1 (Lsd1) organises the trophoblast niche of the early mouse embryo by coordinating migration and invasion of trophoblast stem cells (TSCs). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS5319

Platform:

GPL1261

18 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL17021

6 Samples

Download data: BED, WIG

(Submitter supplied) RNA-Seq for Lsd1-deficient TSCs or treated with Lsd1 inhibitor for 24hrs

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TXT

(Submitter supplied) ChIP-Seq for Lsd1 in TSCs in stemness conditions

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

2 Samples

Download data: BED, WIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

13 Samples

Download data: BW, TXT

(Submitter supplied) Trophoblast stem cells (TSCs) are derived from the trophoectoderm of a blastocyst and can maintain self-renewal in vitro. Meanwhile, essential insights into the molecular mechanisms controlling placental developmental could be gained by using TSCs that can differentiate into the various placental trophoblast cell types in vitro. Esrrb is a transcription factor with pivotal roles in maintaining TSCs’ self-renewal, but the exact transcriptional networks that Esrrb involved in TSCs are largely unknown. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

7 Samples

Download data: BW

(Submitter supplied) Trophoblast stem cells (TSCs) are derived from the trophoectoderm of a blastocyst and can maintain self-renewal in vitro. Meanwhile, essential insights into the molecular mechanisms controlling placental developmental could be gained by using TSCs that can differentiate into the various placental trophoblast cell types in vitro. Esrrb is a transcription factor with pivotal roles in maintaining TSCs’ self-renewal, but the exact transcriptional networks that Esrrb involved in TSCs are largely unknown. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) Three kinds of TSCs with different genotype of mouse Tet2 including Tet2+/-, Tet2-/-and wild-type TSCs were harvested . Total RNA was isolated from cell pellets by Trizol reagent and RNA-Seq library were generated using KAPA Strandard mRNA-Seq Kits according to the manufacturer’s recommendations.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

10 Samples

Download data: TXT

(Submitter supplied) In this study we introduced Sox21 as a new regulator of trophoblast stem cell (TSC) differentiation. The transcriptome of different cell types were analyzed and compared to identify a TSC gene signature.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

20 Samples

Download data: TXT

(Submitter supplied) Mouse trophoblast stem cells (TSCs) proliferate indefinitely in vitro, despite their highly heterogeneous nature. In this study, we sought to characterize TSC colony types by using methods based on cell biology and biochemistry for a better understanding of how TSCs are maintained over multiple passages. Colonies of TSCs could be classified into four major types: type 1 is compact and dome-shaped, type 4 is flattened but with a large multilayered cell cluster, and types 2 and 3 are their intermediates. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10787

45 Samples

Download data: TXT

(Submitter supplied) To analyze the functional relevance of LSD1 in neuroblastic tumors, SH-SY5Y cells were transiently transfected with siRNA directed against LSD1 or with a scrambled control siRNA. Microarray analysis revealed changes in expression that were consistent with these observations 72 hours after LSD1 knock-down. At this time, 28 genes were significantly induced at least 1.5-fold and 29 genes were significantly repressed at least 1.5-fold. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5281

Platform:

GPL570

4 Samples

Download data: CEL

Analysis of SH-SY5Y neuroblastoma cells depleted for lysine-specific demethylase 1 (LSD1). LSD1 is a histone demethylating enzyme. Results provide insight into the role of LSD1 in neuroblastoma.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 protocol sets

Platform:

GPL570

Series:

GSE13273

4 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

24 Samples

Download data: BW

(Submitter supplied) To understand the role of LSD1 in B cell differentiation, mice with B cell conditional deletion of LSD1 were intravenously inoculated with LPS. After 3 days, B220+GL7-CD138- naïve B cells and CD138+ plasmablasts were FACS-sorted from the spleens and RNA-seq was performed to identify LSD1-target regulated genes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: BW, TSV

(Submitter supplied) To understand the role of LSD1 in B cell differentiation, mice with B cell conditional deletion of LSD1 were intravenously inoculated with LPS. After 3 days, B220+GL7-CD138- naïve B cells and CD138+ plasmablasts were FACS-sorted from the spleens and RNA-seq was performed to identify LSD1-target regulated chromatin.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: BW

(Submitter supplied) The effective proliferation and differentiation of Trophoblast Stem Cells (TSCs) is necessary to ensure the normal development of the placenta, which is the key to maintain fetal growth and development during pregnancy. Previous studies have found that knocking out Klf5 affects abnormally trophoderm development, but its regulatory mechanism is unclear. Here we performed klf5 knockdown in TSCs cultured under stem state condition. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21273

22 Samples

Download data: BW, TXT

(Submitter supplied) Trophoblast stem cells represent the stem cell population of the extraembryonic lineage and arise as result of the first cell fate decision. From the blastocyst stage onwards, the extraembryonic lineage is strictly separated from the embryonic lineage by a distinct epigenetic lineage barrier. Recently, it has been shown, that this epigenetic barrier cannot be fully overcome as the expression of TS-determining factors in embryonic stem cells lead to incomplete trans-differentiation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

7 Samples

Download data: TXT

(Submitter supplied) Trophoblast stem cells represent the stem cell population of the extra-embryonic lineage and arise as a result of the first cell fate decision. From blastocyst stage onwards, a distinct epigenetic lineage barrier strictly separates mouse embryonic and extra-embryonic lineages. Recently, it has been shown that this epigenetic barrier cannot be fully overcome as the expression of TS-determining factors in embryonic stem cells lead to incomplete transdifferentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

11 Samples

Download data: TXT

(Submitter supplied) Transcriptome analysis of LSD1-depleted HepG2 cells revealed that LSD1 regulates the expression of glycolytic and mitochondrial metabolism genes. We found that LSD1 is an important regulator of glycolysis and mitochondrial respiration in hepatoma.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

4 Samples

Download data: CEL