GEO DataSets

(Submitter supplied) One of the two X chromosomes in female somatic cells is transcriptionally silenced across cell generations, a classic paradigm of epigenetic regulation.  Although most genes are stably silenced, certain X-linked genes escape X-chromosome inactivation (XCI), providing a fundamental dosage difference between females and males.  A role for chromosome conformation has been proposed in XCI as the process is  accompanied by a massive structural reorganisation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

7 Samples

Download data: BW, NARROWPEAK, TXT

(Submitter supplied) X-chromosome inactivation (XCI) entails a massive structural reorganization of the inactive X (Xi). However the molecular architecture of the Xi is unknown. Here we show that the Xi lacks typical autosomal features such as active/inactive compartments and topologically associating domains (TADs), except around a small number of genes that escape XCI and remain expressed. Escaping genes form TADs and retain DNA accessibility at promoter-proximal and CTCF binding sites, indicating that these loci can avoid Xist-mediated erasure of chromosomal structure. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other; Third-party reanalysis

Platform:

GPL13112

8 Samples

Download data: TAR, TXT

(Submitter supplied) The Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation (XCI), the process by which mammals compensate for unequal numbers of sex chromosomes. During XCI, Xist coats the future inactive X (Xi) and recruits Polycomb Repressive Complex 2 (PRC2) to the X-inactivation center (Xic). Currently unclear is how Xist spreads silencing on a 150 Mb scale. Here we generate high-resolution maps of Xist binding across a developmental time course using CHART-seq. more...

Organism:

Mus musculus

Type:

Other

Platforms:

GPL17021 GPL13112

27 Samples

Download data: BEDGRAPH

(Submitter supplied) RNAseq of SPOC-tethering mESCs.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

27 Samples

Download data: TSV

(Submitter supplied) HiC on Spen-degron TX1072 clones of neural progenitor cells (NPCs). HiC in 2 biological replicates before and after. 24h of auxin treatment.

Organism:

Mus musculus

Type:

Other

Platform:

GPL21103

4 Samples

Download data: MCOOL

(Submitter supplied) RNAseq in ESCs, before and after induction of Xist, with/without deletion of SPEN (auxin treatment).

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

16 Samples

Download data: BW

(Submitter supplied) RNAseq on Spen KO hybrid embryos.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

10 Samples

Download data: BW

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24247 GPL21103 GPL19057

73 Samples

Download data: BW, MCOOL, TXT

(Submitter supplied) RNAseq on Spen-degron TX1072 clones of neural progenitor cells (NPCs). RNAseq in 2 biological replicates at 3 different times of auxin treatment (0h aux, 24h aux, 48h aux).

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: TXT

(Submitter supplied) CUT&RUN on Spen-degron TX1072 mESCs was performed in 2 biological replicates. Cells were treated with doxycycline (1ug/mL) for 0h, 4h, 8h, 24h and 8h doxycycline and auxin (500uM).

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

10 Samples

Download data: BW

(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

Platforms:

GPL21103 GPL19057

69 Samples

Download data: BW

(Submitter supplied) We show that Spen, an Xist binding repressor protein essential for XCI, binds to ancient retroviral RNA transcribed genome-wide, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen inactivation leads to de-repression of endogenous retroviral (ERV) elements in embryonic stem cells, with gain of chromatin accessibility, active histone modifications, and ERV RNA transcription. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21103 GPL19057

28 Samples

Download data: BED, BW

(Submitter supplied) We show that Spen, an Xist binding repressor protein essential for XCI, binds to ancient retroviral RNA transcribed genome-wide, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen inactivation leads to de-repression of endogenous retroviral (ERV) elements in embryonic stem cells, with gain of chromatin accessibility, active histone modifications, and ERV RNA transcription. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

31 Samples

Download data: BW

(Submitter supplied) We show that Spen, an Xist binding repressor protein essential for XCI, binds to ancient retroviral RNA transcribed genome-wide, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen inactivation leads to de-repression of endogenous retroviral (ERV) elements in embryonic stem cells, with gain of chromatin accessibility, active histone modifications, and ERV RNA transcription. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: BED, BW

(Submitter supplied) We show that Spen, an Xist binding repressor protein essential for XCI, binds to ancient retroviral RNA transcribed genome-wide, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen inactivation leads to de-repression of endogenous retroviral (ERV) elements in embryonic stem cells, with gain of chromatin accessibility, active histone modifications, and ERV RNA transcription. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: TXT

(Submitter supplied) Background: During early embryonic development, one of the two X chromosomes in mammalian female cells is inactivated to compensate for a potential imbalance in transcript levels with male cells containing a single X chromosome. We use mouse female Embryonic Stem Cells (ESCs) with nonrandom XCI and polymorphic X chromosomes to study the dynamics of gene silencing over the inactive X chromosome (Xi) by high-resolution allele-specific RNA-Seq. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL13112 GPL11002 GPL19057

20 Samples

Download data: BED, TXT, WIG

(Submitter supplied) To investigate the effect of Smchd1 ablation on de novo X chromosome inactivation (XCI), we derived clonal neural progenitor cells (NPCs) from Smchd1+/+ (wild-type, WT) and Smchd1-/- mouse embryonic stem cells (ES cells; ESC). We generated allele-specific RNA-seq datasets from WT and Smchd1-/- NPCs to examine the effect of Smchd1 ablation on gene silencing. In addition, we produced allele-specific ChIP-seq profiles of H3K4me3, H3K27me3, CTCF, and RAD21 and Xist CHART-seq profiles in WT and Smchd1-/- NPCs to investigate the role of SMCHD1 on the distribution of euchromatin, facultative heterochromatin, architectural proteins, and Xist RNA on the inactive X chromosome (Xi). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other; Third-party reanalysis

Platform:

GPL17021

53 Samples

Download data: BED, BEDGRAPH, BW, TXT

(Submitter supplied) We report the application of Chromosome Conformation Capture Carbon-copy (5C) to a 4.5 Mb stretch of the mouse X chromosome encompassing the X inactivation center locus. We uncover a series of discrete 200kb-1Mb topologically associating domains (TADs). These align with several domain-wide epigenomic features as well as co-regulated gene clusters. 5C analysis in EED and G9A mutants reveal that this segmental organisation in TADs does not relie on the underlying H3K27me3 or H3K9me2 blocks. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL11002

20 Samples

Download data: FA, TXT

(Submitter supplied) Embryonic stem cells (ESC) are derived from the inner cell mass of the blastocyst in the presence of leukemia inhibitory factor (LIF). In vivo these cells then differentiate into epi stem cells (EpiSC) that can be derived from the Epiblast in presence of Fgf2 and ActivinA. In this study, female ESCs cultured in 2i medium have been differentiated into EpiSC for 3.5 days in vitro by addition of Fgf2 and Activin A. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6193

17 Samples

Download data: CEL

(Submitter supplied) The binding of the transcriptional regulator CTCF to the genome has been implicated in the formation of topologically associated domains (TADs). However, the general mechanisms of folding the genome into TADs are not fully understood. Here, we tested the effects of deleting a CTCF-rich locus on TAD boundary formation. Using genome-wide chromosome conformation capture (Hi-C), we focus on one TAD boundary on chromosome X harboring ~15 CTCF binding sites, and located at the long non-coding RNA (lncRNA) locus Firre. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

4 Samples

Download data: BED, MATRIX