GEO DataSets

(Submitter supplied) Genomic DNA from 6 pure EC and 2 normal testis was fragmented and immunoprecipitated with anti-5mC monoclonal antibodies by MeDIP. After IP, DNA was purified and amplified using Whole Genome Amplification. Subsequently, DNA was biotin-labeled and hybridized to Human Tiling Array 2.0R Chips (Affymetrix) according to the manufacturer’s instruction. Raw data (CEL files) were normalized and analyzed by TAS (Affymetrix). more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

7 related Platforms

223 Samples

Download data: BED, CEL

(Submitter supplied) Non-coding RNAs (ncRNAs) play major roles in proper chromatin organization and function. Senescence, a strong anti-proliferative process and a major anti-cancer barrier, is associated with dramatic chromatin reorganization in heterochromatin foci. Here, we analyze strand-specific transcriptome changes during oncogene-induced human senescence. Strikingly, while differentially-expressed RNAs are mostly repressed during senescence, ncRNAs belonging to the recently described vlincRNA (very long intergenic ncRNA) class are mainly activated. more...

Organism:

Homo sapiens

Type:

Expression profiling by genome tiling array

Platform:

GPL4910

8 Samples

Download data: CEL, CHP

(Submitter supplied) Nuclear processing and quality control of eukaryotic RNA is mediated by the multi-subunit RNA exosome, which utilizes accessory factors to regulate its enzymatic activity. However, the mechanism of exosome recruitment to its ribonucleoprotein (RNP) targets remains poorly understood. Here we disclose a physical link between the human nuclear RNA exosome and the cap-binding complex (CBC). The CBC associates with the ARS2 protein to form CBC-ARS2 (CBCA), and then further connects together with the uncharacterized ZC3H18/NHN1 protein to the nuclear exosome targeting (NEXT) complex, forming CBC-NEXT (CBCN). more...

Organism:

Homo sapiens

Type:

Expression profiling by genome tiling array

Platform:

GPL4910

10 Samples

Download data: CEL, TXT, XLS

(Submitter supplied) The nuclear cap-binding complex (CBC) stimulates multiple steps in several RNA maturation pathways, but how it functions in humans is incompletely understood. For small capped RNAs like pre-snRNAs, the CBC recruits PHAX. Here, we identify the CBCAP complex, composed of CBC, Ars2 and PHAX, and show that both CBCAP and CBC-Ars2 complexes can be reconstituted from recombinant proteins. Ars2 stimulates PHAX binding to the CBC as well as snRNAs 3'-end processing, hereby coupling maturation with export. more...

Organism:

Homo sapiens

Type:

Expression profiling by genome tiling array; Expression profiling by array

Platforms:

GPL6244 GPL4910

12 Samples

Download data: CEL, TXT, XLS

(Submitter supplied) Here we present an approach for the mapping of unmethylated DNA. Our technique is based on DNA methyltransferase-directed transfer of activated groups (mTAG) and covalent biotin tagging of unmodified CpG sites followed by affinity enrichment and interogation on tiling microarrays or next generation sequencing.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Other

Platforms:

GPL4913 GPL4916 GPL4910

90 Samples

Download data: BED, BEDGRAPH, CEL

(Submitter supplied) Altered gene expression patterns in human diseases reflect perturbations in the transcriptional networks that regulate cellular state. In breast cancer, Nuclear Receptors (NRs) play a prominent role in governing gene expression. NRs have prognostic utility and are therapeutically important targets. Here we describe a complete regulatory map for twenty-four NR proteins that are expressed in the breast cancer cell line MCF-7, as well as fourteen additional breast cancer associated transcription factors (TFs) and six key chromatin state markers.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

7 related Platforms

42 Samples

Download data: BAR, BED, CEL

(Submitter supplied) Altered gene expression patterns in human diseases reflect perturbations in the transcriptional networks that regulate cellular state. In breast cancer, Nuclear Receptors (NRs) play a prominent role in governing gene expression. NRs have prognostic utility and are therapeutically important targets. Here we describe a complete regulatory map for twenty-four NR proteins that are expressed in the breast cancer cell line MCF-7, as well as fourteen additional breast cancer associated transcription factors (TFs) and six key chromatin state markers. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

7 related Platforms

238 Samples

Download data: BAR, BED, CEL

(Submitter supplied) DNA from Epstein-Barr virus (EBV)-transformed lymphocyte cell lines (LCLs) has proven very useful for studies of genetic sequence polymorphisms. Whether EBV-LCL DNA is suitable for methylation studies is less clear. We conduct a genome-wide methylation investigation using an array set with 45 million probes to investigate the methylome of EBV-LCL DNA and technical duplicates of whole blood (WB) DNA from the same 10 individuals. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

7 related Platforms

210 Samples

Download data: CEL, TXT

(Submitter supplied) FoxA1, in conjunction with MYBL2 and CREB1, governs G1/S cell-cycle transition in androgen-independent prostate cancer .

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

7 related Platforms

21 Samples

Download data: CEL, TXT

(Submitter supplied) Dysregulation of Wnt signaling is involved in carcinogenesis, mainly through activation of beta-catenin/TCF target genes. Although aberrant activation of several Wnt target genes, including CCND1 and MYC, has been reported as promoting proliferation of cancer cells, it is hardly enough to understand malignant phenotypes of cancer cells with aberrant Wnt signaling. To elucidate the transcriptional regulation of beta-catenin/TCF target genes, we examined binding of beta-catenin (BC) to DNA by chromatin immunoprecipitation linked to genome tiling array (ChIP-on-chip).

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4910

1 Sample

Download data: BAR, CEL

(Submitter supplied) The objective of this study was to identify how histone modifications are differentially marked at promoter and enhancer elements in hESCs before and after differentiation to understand the regulatory mechanisms that defined pluripotency and early differentiation.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

29 related Platforms

94 Samples

Download data: CEL, GFF, PAIR

(Submitter supplied) DNA amplification, particularly of chromosomes 8 and 11, occurs frequently in breast cancer and is a key factor in tumorigenesis, often associated with poor prognosis. The mechanisms involved in the amplification of these regions are not fully understood. Studies from model systems have demonstrated that palindrome formation can be an early step in DNA amplification, most notably seen in the breakage-fusion-bridge (BFB) cycle. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array; Genome variation profiling by SNP array

8 related Platforms

31 Samples

Download data: BAR, CEL, CNCHP

(Submitter supplied) p73 is a p53 family transcription factor that plays critical roles during development and tumor suppression. We analyzed p73 activity using a combination of ChIP-on-Chip and gene expression profiling, both at baseline and after treatment with the mTOR inhibitor rapamycin. This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

8 related Platforms

22 Samples

Download data: BAR, CEL

(Submitter supplied) p73 is a p53 family transcription factor that plays critical roles during development and tumor suppression. We analyzed p73 activity using a combination of ChIP-on-Chip and gene expression profiling, both at baseline and after treatment with the mTOR inhibitor rapamycin. We report the first comprehensive analysis of p73 binding across the genome. Furthermore, we re-analyzed this p73 cistrome after perturbation with rapamycin, an inhibitor of mTOR and inducer of p73. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

7 related Platforms

14 Samples

Download data: BAR, CEL

(Submitter supplied) Estrogen receptor alpha (ERα) expression in breast cancer is predictive of response to endocrine therapy, however resistance is common in ERα-positive tumors that over-express the growth factor receptor ERBB2. Even in the absence of estrogen, ERα can be activated by growth factors including the epidermal growth factor (EGF). EGF induces a transcriptional program distinct from estrogen, however the mechanism of the stimulus-specific response is unknown. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by array

8 related Platforms

47 Samples

Download data: BAR, CEL

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

Organism:

Homo sapiens

Type:

Methylation profiling by array; Expression profiling by array; Methylation profiling by genome tiling array

9 related Platforms

36 Samples

Download data: CEL

(Submitter supplied) HPV-associated head and neck cancers (HNSCCs) have a distinct risk profile and appreciate a prognostic advantage compared to HPV-negative HNSCC. To assess the genome-wide methylation changes in HPV(+) and HPV(-) tumors, we analyzed DNA methylation and expression patterns in two HPV(+) and two HPV(-) cell lines. HPV(+) tumors have overall higher DNA methylation in genic and LINE1 regions than HPV(-) tumors, and polycomb repressive complex 2 (PRC2) targets tend to be much more highly methylated in HPV(+) cells.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

7 related Platforms

28 Samples

Download data: BED, CEL, TXT

(Submitter supplied) Using chromatin immunoprecipitation and high-resolution tiling arrays covering the human genome, we render a genome-wide map of p73 DNA binding sites in ME180 human cervical carcinoma cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

7 related Platforms

7 Samples

Download data: BAR, CEL, TXT, XLS

(Submitter supplied) Surprisingly few pathways signal between cells, raising questions about mechanisms for tissue-specific responses. In particular, Wnt ligands signal in many mammalian tissues, including the intestinal epithelium, where constitutive signaling causes cancer. Genome-wide analysis of DNA cis-regulatory regions bound by the intestine-restricted transcription factor CDX2 in colonic cells uncovered highly significant over-representation of sequences that bind TCF4, a transcriptional effector of intestinal Wnt signaling. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by array

8 related Platforms

56 Samples

Download data: BAR, CEL, TXT

(Submitter supplied) Androgen signaling through the androgen receptor (AR), a ligand-dependent transcription factor within the steroid receptor superfamily, plays an important role in the development and maintenance of many tissues. In muscle, androgens act as anabolic agents that increase both muscle mass and strength; however, a key unanswered question is the mechanism through which AR-mediated gene expression leads to these effects. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

7 related Platforms

21 Samples

Download data: BED, CEL