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Links from GEO DataSets

Items: 20

1.

Smchd1 regulates autosomal genes subject to monoallelic expression

(Submitter supplied) Analysis of the genes that escape silencing in the MommeD1 allele of Smchd1
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6885
16 Samples
Download data: TXT
Series
Accession:
GSE44958
ID:
200044958
2.

Genome wide RNA-seq analysis of Smchd1 wild type and mutant

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
16 Samples
Download data
Series
Accession:
GSE44669
ID:
200044669
3.

Genome wide RNA-seq analysis of E14.5 Smchd1 wild type and mutant placenta

(Submitter supplied) We report the deregulation of expression in Fi (C57Bl6/J x FVB/n) E14.5 male mouse placenta are that homozygous for a mutant allele of the Smchd1 gene (ie Smchd1MommeD1/MommeD1).
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
10 Samples
Download data: CSV, TXT
Series
Accession:
GSE44668
ID:
200044668
4.

Genome wide RNA-seq analysis of E9.5 Smchd1 wild type and mutant embryos

(Submitter supplied) We report the deregulation of expression in E9.5 male mouse embryos are that homozygous for a mutant allele of the Smchd1 gene (ie Smchd1MommeD1/MommeD1).
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
6 Samples
Download data: TXT
Series
Accession:
GSE44665
ID:
200044665
5.

Investigating the role of SMCHD1 in regulating clustered protocadherin (Pcdh) and Hox genes

(Submitter supplied) To investigate the effect of Smchd1 ablation on clustered Pcdh and Hox genes, we generated ChIP-seq profiles of EZH2 in clonal neural progenitor cells (NPCs) from Smchd1+/+ (wild-type, WT) and Smchd1-/- mouse embryonic stem (ES) cells. We also reanalyzed previously published Hi-C data (GSE99991) (Wang et al., 2018, Cell) in these two cell lines.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL17021
2 Samples
Download data: BW
6.

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
7.

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
8.

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
9.

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
10.

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
11.

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
12.

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
13.

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
14.

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
Download data
Series
Accession:
GSE112097
ID:
200112097
15.

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
16.

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
17.

Random monoallelic expression in the mouse: SNP array data

(Submitter supplied) Random monoallelic expression is defined by the allele-specific expression of genes, and by the fact that for an individual cell this monoallelic expression is neither obligate nor necessarily coordinated with the allelic expression in other cells. In order to find novel examples of random monoallelic expression in mouse, we did a transcriptome-wide survey of allele-specific gene expression in two different immortalized cell types. more...
Organism:
Mus musculus
Type:
SNP genotyping by SNP array
Platform:
GPL15197
48 Samples
Download data: CEL, TXT
Series
Accession:
GSE35678
ID:
200035678
18.

Chromosome-wide profiling of X-inactivation status and epigenetic regulation in opossum fetal brain and placenta

(Submitter supplied) Evidence from a few genes of diverse species suggests that marsupial X-chromosome inactivation (XCI) is characterized by exclusive, but leaky, inactivation of the paternally derived X chromosome. To comprehensively study the mechanism of marsupial XCI, we profiled parent-of-origin-specific-allele expression, DNA methylation, and histone modifications in opossum fetal brain and extra-embryonic membranes. more...
Organism:
Monodelphis domestica
Type:
Expression profiling by high throughput sequencing
Platform:
GPL15381
16 Samples
Download data: TXT
Series
Accession:
GSE45211
ID:
200045211
19.

Chromosome-wide profiling of X-inactivation status and epigenetic regulation in fetal brain

(Submitter supplied) Evidence from a few genes of diverse species suggests that marsupial X-chromosome inactivation (XCI) is characterized by exclusive, but leaky, inactivation of the paternally derived X chromosome. To comprehensively study the mechanism of marsupial XCI, we profiled parent-of-origin-specific-allele expression, DNA methylation, and histone modifications in opossum fetal brain and extra-embryonic membranes. more...
Organism:
Monodelphis domestica
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL15381
8 Samples
Download data: BED
Series
Accession:
GSE45186
ID:
200045186
20.

Allelic imbalance is a prevalent and tissue-specific feature of the mouse transcriptome

(Submitter supplied) We perform a systematic classification of allelic imbalance in mouse hybrids derived from reciprocal crosses of divergent strains. We observe that deviation from balanced biallelic expression is common, occurring in ~20% of the mouse transcriptome. Allelic imbalance attributed to genotype is by far the most prevalent class and typically is tissue-specific. However, some genotype-based imbalance is maintained across tissues and is associated with greater genetic variation, especially in 5’ and 3’ termini of transcripts. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL13112
11 Samples
Download data: BW
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