Similar studies for GEO DataSets (Select 200040880) - GEO DataSets

Select item 2000408801.

The effect on gene expression of Smchd1 deletion in end stage lymphomas

(Submitter supplied) Smchd1 appears to act as a tumour suppressor in the Eµ-Myc B cell lymphoma model. We find gene expression differences are most pronounced in the premalignant cells, and observe more variability in end stage lymphomas. We always detect a small number of clustered genes and imprinted genes as differentially expressed, along with others involved in tumorigenesis.

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL6887
12 Samples

Download data: TXT

Series

Accession:: GSE40880

ID:: 200040880

Select item 2000409922.

The effect on gene expression of Smchd1 deletion in various cell types

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

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL6887
60 Samples

Download data

Series

Accession:: GSE40992

ID:: 200040992

Select item 2000408813.

The effect on gene expression of Smchd1 deletion in premalignant pre-B cells

(Submitter supplied) Smchd1 appears to act as a tumour suppressor in the Eµ-Myc B cell lymphoma model. We find gene expression differences are most pronounced in premalignant cells. We always detect a small number of clustered genes and imprinted genes as differentially expressed, along with others involved in tumorigenesis.

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL6887
12 Samples

Download data: TXT

Series

Accession:: GSE40881

ID:: 200040881

Select item 2000408794.

The effect on gene expression of Smchd1 deletion in pre-B cells from E17.5 Eµ-Myc embryos

(Submitter supplied) Smchd1 appears to act as a tumour suppressor in the Eµ-Myc mouse B cell lymphoma model. We find a small number of gene expression differences at E17.5 in the pre-B cells, before phenotypic differences are observed.

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL6887
6 Samples

Download data: TXT

Series

Accession:: GSE40879

ID:: 200040879

Select item 2000407345.

The effect on gene expression of Smchd1 deletion in primary MEFs, transformed MEFs and MEF tumours

(Submitter supplied) Smchd1 appears to act as a tumour suppressor in the transformed fibroblast model. We find gene expression differences are most pronounced in the transformed MEFs. We always detect a small number of clustered genes and imprinted genes as differentially expressed, along with others involved in tumorigenesis.

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL6887
30 Samples

Download data: TXT

Series

Accession:: GSE40734

ID:: 200040734

Select item 2001120976.

Role of SmcHD1 in the establishment of the epigenetic states required for the maintenance of X chromosome inactivation

(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:: GPL18480 GPL11002
8 Samples

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Series

Accession:: GSE112097

ID:: 200112097

PubMed Similar studies

Select item 2001120967.

Role of SmcHD1 in the establishment of the epigenetic states required for the maintenance of X chromosome inactivation [ChIP-seq]

(Submitter supplied) It has been shown that functional deficiency of SmcHD1, a noncanonical member of SMC family proteins, results in derepression of X-inactivated genes in postimplantation female mouse embryos. In this study, we found that derepression of X-inactivated genes accompanied a local reduction in the enrichment of H3K27me3 in mouse embryonic fibroblasts (MEFs) prepared from female fetuses deficient for SmcHD1.

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL11002
4 Samples

Download data: TXT

Series

Accession:: GSE112096

ID:: 200112096

PubMed Similar studies SRA Run Selector

Select item 2001120958.

Role of SmcHD1 in the establishment of the epigenetic states required for the maintenance of X chromosome inactivation [RNA-seq]

(Submitter supplied) It has been shown that functional deficiency of SmcHD1, a noncanonical member of SMC family proteins, results in derepression of X-inactivated genes in postimplantation female mouse embryos. In this study, we found that derepression of X-inactivated genes accompanied a local reduction in the enrichment of H3K27me3 in mouse embryonic fibroblasts (MEFs) prepared from female fetuses deficient for SmcHD1.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18480
4 Samples

Download data: TXT

Series

Accession:: GSE112095

ID:: 200112095

PubMed Similar studies SRA Run Selector

Select item 2000657499.

Genome-wide binding and mechanistic analyses of Smchd1 mediated epigenetic regulation

(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; Methylation profiling by high throughput sequencing

Platform:: GPL13112
34 Samples

Download data: TXT

Series

Accession:: GSE65749

ID:: 200065749

PubMed Full text in PMC Similar studies

Select item 20006574810.

Genome-wide binding and mechanistic analyses of Smchd1 mediated epigenetic regulation [ChIP-Seq, MBD-Seq]

(Submitter supplied) Purpose: The aim of this study is (1) to identify the chromatin occupancy of the epigenetic regulator Smchd1 in neural stem cells (NSCs) derived from E14.5 mouse brain; (2) to profile key epigenetic marks H3K4me3, H3K27me3 and DNA methylation in wild type and Smchd1 null NSCs; (3) to identify the chromatin occupancy of Ctcf in wild type and Smchd1 null NSCs. Methods: Chromatin immunoprecipitation for Smchd1, H3K4me3, H3K27me3 and Ctcf was performed essentially as in (Nelson et al. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:: GPL13112
28 Samples

Download data: BED, BEDGRAPH

Series

Accession:: GSE65748

ID:: 200065748

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006574711.

Genome-wide binding and mechanistic analyses of Smchd1 mediated epigenetic regulation [RNA-Seq]

(Submitter supplied) Purpose: The aim of this study is to identify genes that are under the transcriptional control of the epigenetic regulator Smchd1 in neural stem cells (NSCs) derived from E14.5 mouse brain Methods: Total RNA was extracted using an AllPrep DNA/RNA Mini Kit (Qiagen) from cultured neural stem cells derived from male mouse E14.5 brains either wild-type or null for Smchd1. 1 µg total RNA was used to generate sequencing libraries for whole transcriptome analysis with Illumina’s TruSeq RNA Sample Preparation Kit v2 as per standard protocols. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13112
6 Samples

Download data: TXT

Series

Accession:: GSE65747

ID:: 200065747

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20020118912.

SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice

(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:: GPL13112 GPL21493
16 Samples

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Series

Accession:: GSE201189

ID:: 200201189

PubMed Similar studies

Select item 20020118813.

SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice [RNA-seq]

(Submitter supplied) Stable silencing of the inactive X chromosome (Xi) in female mammals is crucial for the development of embryos and their postnatal health. SmcHD1 is essential for stable silencing of the Xi, and its functional deficiency results in derepression of many X-inactivated genes. Although SmcHD1 has been suggested to play an important role in the formation of higher-order chromatin structure of the Xi, the underlying mechanism is largely unknown. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13112
4 Samples

Download data: TXT

Series

Accession:: GSE201188

ID:: 200201188

PubMed Similar studies

Select item 20020118714.

SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice [ChIP-seq]

(Submitter supplied) Stable silencing of the inactive X chromosome (Xi) in female mammals is crucial for the development of embryos and their postnatal health. SmcHD1 is essential for stable silencing of the Xi, and its functional deficiency results in derepression of many X-inactivated genes. Although SmcHD1 has been suggested to play an important role in the formation of higher-order chromatin structure of the Xi, the underlying mechanism is largely unknown. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21493
12 Samples

Download data: TXT

Series

Accession:: GSE201187

ID:: 200201187

PubMed Similar studies

Select item 20011593315.

In situ Hi-C in Smchd1 wild-type and Smchd1 deleted neural stem cells. [II]

(Submitter supplied) We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq, chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. more...

Organism:: Mus musculus

Type:: Other

Platform:: GPL19057
4 Samples

Download data: H5

Series

Accession:: GSE115933

ID:: 200115933

PubMed Similar studies SRA Run Selector

Select item 20011593216.

RRBS in Smchd1 control and Smchd1 deleted male and female neural stem cells.

(Submitter supplied) We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq, chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. more...

Organism:: Mus musculus

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL19057
4 Samples

Download data: TXT

Series

Accession:: GSE115932

ID:: 200115932

PubMed Similar studies SRA Run Selector

Select item 20011204617.

Allele-specific H3K27me3, H3K27ac and Ctcf ChIP-seq in Smchd1 control and Smchd1 deleted female neural stem cells. [H3K27ac]

(Submitter supplied) We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq, chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL19057
4 Samples

Download data: TXT

Series

Accession:: GSE112046

ID:: 200112046

PubMed Similar studies SRA Run Selector

Select item 20011204518.

Allele-specific H3K27me3, H3K27ac and Ctcf ChIP-seq in Smchd1 control and Smchd1 deleted female neural stem cells. [H3K27me3]

(Submitter supplied) We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq, chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL19057
8 Samples

Download data: TXT

Series

Accession:: GSE112045

ID:: 200112045

PubMed Similar studies SRA Run Selector

Select item 20011204319.

Allele-specific RNA-seq in Smchd1 control and Smchd1 deleted female neural stem cells.

(Submitter supplied) We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq, chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL19057
4 Samples

Download data: TXT

Series

Accession:: GSE112043

ID:: 200112043

PubMed Similar studies SRA Run Selector

Select item 20011204120.

RNA-seq in Smchd1 wild-type and Smchd1 null presomitic mesoderm from E9.5 embryos

(Submitter supplied) We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq, chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL19057
7 Samples

Download data: TXT

Series

Accession:: GSE112041

ID:: 200112041

PubMed Similar studies SRA Run Selector

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