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) 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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; Homo sapiens

Type:

Methylation profiling by genome tiling array; Methylation profiling by high throughput sequencing

7 related Platforms

795 Samples

Download data: BED, CEL

(Submitter supplied) 5-hydroxymethylcytosine (5-hmC), a derivative of 5-methylcytosine (5-mC), is abundant in the brain for unknown reasons. We mapped the genomic distribution of 5-hmC and 5-mC in human and mouse tissues using glucosylation of 5-hmC coupled with restriction enzyme digestion, and interrogation on microarrays. We detected 5-hmC enrichment in genes with synapse-related functions in the brain. We also identified significant, tissue-specific differential distributions of these DNA modifications at the exon-intron boundary, in both human and mouse. more...

Organism:

Homo sapiens; Mus musculus

Type:

Methylation profiling by genome tiling array

6 related Platforms

786 Samples

Download data: BED, CEL

(Submitter supplied) Cytosine 5-modification is a widespread epigenetic mark in eukaryote genomes including humans, but its large scale populational studies are hampered by substantial limitations of the existing analytical techniques. We have developed a new approach for mapping of the unmodified fraction of the genome, i.e. DNA unmethylome, which is based on covalent tagging of unmodified CpG sites with biotin. Sequence-specific tagging of DNA was achieved by using an engineered version of the SssI cytosine-5 methyltransferase and a synthetic analog of the S-adenosylmethionine cofactor carrying a transferable 6-aminohex-2-ynyl group. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL4914

24 Samples

Download data: 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) 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) In eukaryotes, U1 small nuclear ribonucleoprotein (snRNP) forms spliceosomes in equal stoichiometry with U2, U4, U5 and U6 snRNPs; however, its abundance in human far exceeds that of the other snRNPs. Here we used antisense morpholino oligonucleotide to U1 snRNA to achieve functional U1 snRNP knockdown in HeLa cells, and identified accumulated unspliced pre-mRNAs by genomic tiling microarrays. In addition to inhibiting splicing, U1 snRNP knockdown caused premature cleavage and polyadenylation in numerous pre-mRNAs at cryptic polyadenylation signals, frequently in introns near (<5 kilobases) the start of the transcript. more...

Organism:

Homo sapiens

Type:

Expression profiling by genome tiling array

Platform:

GPL4914

3 Samples

Download data: BAR, CEL

(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

(Submitter supplied) FOXP3 is essential for the stability and function of nTReg. We have characterised the FOXP3-dependent cis-regulatory network through a combination of whole genome ChIP-on-chip and transcriptional profiling of primary human nTreg cells . Human nTreg cells were isolated from cord blood and expanded ex vivo (day9). These analyses identified approximately 8,000 high quality FOXP3 binding sites the majority (85%) of which were located in proximity to annotated genes . more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

7 related Platforms

7 Samples

Download data: BED, CEL