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Links from GEO DataSets

Items: 20

1.

Reduced levels of two modifiers of epigenetic gene silencing, Dnmt3a and Trim28, cause increased phenotypic noise.

(Submitter supplied) Inbred individuals reared in controlled environments display considerable variance in many complex traits. The underlying cause of this variability has been an enigma, hence the term intangible variation. Here we show that two modifiers of epigenetic gene silencing play a critical role in the process. Inbred mice heterozygous for a null mutation in DNA methyltransferase 3a (Dnmt3a) or tripartite motif protein 28 (Trim28), show greater coefficients of variance in body weight than their wildtype littermates. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6885
16 Samples
Download data: TXT
Series
Accession:
GSE23512
ID:
200023512
2.

Kap1 in liver physiology

(Submitter supplied) Hepatocellular carcinoma (HCC) represents the fifth most common form of cancer worldwide and carries a high mortality rate due to lack of effective treatment. Males are eight times more likely to develop HCC that females, an effect largely driven by sex hormones, albeit through still poorly understood mechanisms. We previously identified TRIM28, a scaffold protein capable of recruiting a number of chromatin modifiers, as a crucial mediator of sexual dimorphism in the liver, with Trim28hep-/- mice displaying sex-specific transcriptional deregulation of a wide range of bile and steroid metabolism genes and development of liver adenomas in males. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
6 Samples
Download data: TXT
Series
Accession:
GSE86389
ID:
200086389
3.

TRIM28 is essential for erythroblast differentiation in the mouse

(Submitter supplied) We discovered that Trim28 genetic loss in the adult mouse leads to defective immature erythropoiesis in the bone marrow and consequently to anemia.We further found that TRIM28 controls erythropoiesis in a cell-autonomous manner by inducibly deleting Trim28 exclusively in hematopoietic cells. Finally, in the absence of TRIM28 we observed increased apoptosis as well as diminished expression of multiple erythroid transcription factors and heme biosynthetic enzymes in immature erythroid cells. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
9 Samples
Download data: TXT
Series
Accession:
GSE49843
ID:
200049843
4.

Critical role for TRIM28 and HP1beta/gamma in the epigenetic control of T cell metabolic reprograming and effector differentiation

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL17021 GPL13112 GPL17400
90 Samples
Download data: CEL
Series
Accession:
GSE140448
ID:
200140448
5.

PolII ChIP-Seq performed on naïve WT and TRIM28KO CD4 T cells

(Submitter supplied) Critical role for TRIM28 and HP1b/g in the epigenetic control of T cell metabolic reprogramming and effector differentiation
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
8 Samples
Download data: GFF
Series
Accession:
GSE140447
ID:
200140447
6.

H3K9me3 and H3K9Ac ChIP-Seq performed on naïve WT and TRIM28KO CD4 T cells

(Submitter supplied) Critical role for TRIM28 and HP1b/g in the epigenetic control of T cell metabolic reprogramming and effector differentiation
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17021
16 Samples
Download data: BED
Series
Accession:
GSE140446
ID:
200140446
7.

Transcriptome analysis of naïve or stimulated WT and TRIM28 KO CD4 T cells (RNA-seq)

(Submitter supplied) Critical role for TRIM28 and HP1b/g in the epigenetic control of T cell metabolic reprogramming and effector differentiation The study explores the role of gene silencing by TRIM28, an adaptor protein for histone binding modules , in CD4 T cell function.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
6 Samples
Download data: TXT
Series
Accession:
GSE140445
ID:
200140445
8.

Transcriptome analysis of naïve or stimulated WT and TRIM28 KO CD4 T cells (Affymetrix)

(Submitter supplied) Critical role for TRIM28 and HP1b/g in the epigenetic control of T cell metabolic reprogramming and effector differentiation The study explores the role of gene silencing by TRIM28, an adaptor protein for histone binding modules , in CD4 T cell function.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL17400
24 Samples
Download data: CEL
Series
Accession:
GSE140444
ID:
200140444
9.

Transcriptome analysis of WT and TRIM28 KO CD4 T cells, naïve or stimulated with anti-CD3 (plate-bound) and anti-CD28 (soluble) in Th0, Th1, Th2, Th17 or Treg conditions

(Submitter supplied) Critical role for TRIM28 and HP1b/g in the epigenetic control of T cell metabolic reprogramming and effector differentiation The study explores the role of gene silencing by TRIM28, an adaptor protein for histone binding modules , in CD4 T cell function.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL17400
36 Samples
Download data: CEL
Series
Accession:
GSE140443
ID:
200140443
10.

WTX interacts with the transcriptional regulator TRIM28 to mediate cellular differentiation

(Submitter supplied) WTX encodes a tumor suppressor implicated in Wilms tumor and in mesenchymal differentiation, with distinct functions in the cytoplasm, at the plasma membrane and in the nucleus. Here we report that the transcriptional corepressor TRIM28 is the major binding partner for nuclear WTX. The WTX-TRIM28 interaction supports chromatin binding by TRIM28, enhancing transcriptional silencing of some TRIM28 target sequences. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14759
5 Samples
Download data: XLS
Series
Accession:
GSE60418
ID:
200060418
11.

The evolutionary capacitor HSP90 buffers the regulatory effects of mammalian endogenous retroviruses.

(Submitter supplied) The molecular chaperone heat shock protein 90 (HSP90) is thought to buffer genetic variation uncoupling phenotypic outcome from individual genotypes. HSP90 thus acts as an evolutionary capacitor by facilitating an accumulation of natural genetic variation. The molecular mechanism underlying the buffering ability is unclear, and HSP90-contingent genetic variation maps both to coding and non-coding parts of the genome. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
18 Samples
Download data: TXT
Series
Accession:
GSE87119
ID:
200087119
12.

Comparison of gene expression in Wild type and T cell-specific conditional Trim28 KO in TCR stimulated and un-stimulated naive CD4 positive and T regulatory cells

(Submitter supplied) A microarray study was performed in unstimulated and TCR-stimulated CD4 + T cells and Treg in wild type and conditional Trim28 KO mice to identify genes that are regulated by Trim28. These experiments constitute a portion of the study described below: Paper Abstract: Peripheral T cell activation and differentiation into specialized effectors are regulated by TCR- and cytokine-mediated signals that induce clonal expansion and unique transcriptional factors. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL7202
24 Samples
Download data: TXT
Series
Accession:
GSE32224
ID:
200032224
13.

Protein O-GlcNAcylation Silences Methylated Promoters in Mammalian Genomes

(Submitter supplied) Methylated mammalian promoters are transcriptionally silenced even in the presence of all the factors required for their expression. Repression requires the assembly of a methylation-dependent silencing complex that contains the TRIM28 (also known as KAP1 and TIF1β) protein. An internally controlled interaction screen identified O-linked β-N-acetylglucosamine transferase (O-GlcNAc transferase or OGT) as a protein that was complexed with TRIM28 in wild type em-bryonic stem cells but not in Dnmt1-/- cells that had severely demethylated genomes. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL21103
13 Samples
Download data: BW, TXT
Series
Accession:
GSE93539
ID:
200093539
14.

Expression analysis of wt and maternal Trim28 mutant E3.5 embryos

(Submitter supplied) We performed RNAseq on 4 individual E3.5 control and maternal Trim28 blastocysts respectively in order to detect transcriptional differences amog the 2 cohorts which are to be linked to epigentic reprogramming defcts at early stages.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
8 Samples
Download data: BW
Series
Accession:
GSE87504
ID:
200087504
15.

TRIM28 and novel interacting KRAB-ZNFs preserve self-renewal of human pluripotent stem cells through H3K9me3 and DNA methylation mediated repression of pro-differentiation genes

(Submitter supplied) Reprogramming to induced pluripotent stem cells (iPSCs) and differentiation of pluripotent stem cells (PSCs) are primarily regulated by epigenetic machinery. Tripartite motif protein 28 (TRIM28), a universal mediator of Krüppel-associated box domain zinc fingers (KRAB-ZNFs), is known to regulate both processes, however exact mechanism and identity of participating KRAB-ZNF genes remains unknown. Here, using a novel reporter system, we first showed that TRIM28/KRAB-ZNFs alter DNA methylation patterns in addition to H3K9me3 to cause gene repression during reprogramming. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16791
24 Samples
Download data: BED
Series
Accession:
GSE97403
ID:
200097403
16.

Comparison of methylation profile of human somatic and pluripotent stem cells

(Submitter supplied) Reprogramming to induced pluripotent stem cells (iPSCs) and differentiation of pluripotent stem cells (PSCs) are primarily regulated by epigenetic machinery. Tripartite motif protein 28 (TRIM28), a universal mediator of Krüppel-associated box domain zinc fingers (KRAB-ZNFs), is known to regulate both processes, however exact mechanism and identity of participating KRAB-ZNF genes remains unknown. Here, using a novel reporter system, we first showed that TRIM28/KRAB-ZNFs alter DNA methylation patterns in addition to H3K9me3 to cause gene repression during reprogramming. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
13 Samples
Download data: TXT
Series
Accession:
GSE95096
ID:
200095096
17.

WGBS assessment of global methylation alterations in Dnmt3a1KO , Dnmt3a2KO, Dnmt3aKO, Tet1KO and DKO mouse embryonic stem cells

(Submitter supplied) Using WGBS we assessed global DNA methylation changes in Dnmt3a1KO/Dnmt3a2KO/Dnmt3aKO/Tet1KO/DKO mouse embryonic stem cells. Compared with WT cells, Dnmt3aKO cells but not Dnmt3bKO cells showed genome-wide hypomethylation.
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL13112
4 Samples
Download data: BW
Series
Accession:
GSE112312
ID:
200112312
18.

Genome-wide maps of histone modifications (SpikeIn) and Suz12 in WT, Dnmt3a-/-, Tet1-/- J1 and DKO ES cells.

(Submitter supplied) Using ChIP-seq to assess changes of histone modifications in response to Dnmt3a or Tet1 deficiency.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
12 Samples
Download data: BW
Series
Accession:
GSE112311
ID:
200112311
19.

The role of DNMT3A and TET1 in regulating promoter epigenetic landscapes

(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
Platforms:
GPL19057 GPL13112
61 Samples
Download data: BW
Series
Accession:
GSE100957
ID:
200100957
20.

WGBS assessment of global methylation alterations in Dnmt3aKO or Dnmt3bKO mouse embryonic stem cells

(Submitter supplied) Using WGBS we assessed global DNA methylation changes in Dnmt3aKO or Dnmt3bKO mouse embryonic stem cells. Compared with WT cells, Dnmt3aKO cells but not Dnmt3bKO cells showed genome-wide hypomethylation.
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL13112
9 Samples
Download data: BED
Series
Accession:
GSE100956
ID:
200100956
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