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Links from GEO DataSets

Items: 20

1.

CG methylated microarrays identify novel methylated sequence bound by the CEBPB|ATF4 heterodimer that are active in vivo

(Submitter supplied) To evaluate the effect of CG methylation on DNA binding of sequence-specific B-ZIP transcription factors (TFs) in a high-throughput manner, we enzymatically methylated the cytosine in the CG dinucleotide on protein binding microarrays. Two Agilent DNA array designs were used. One contained 40,000 features using de Bruijn sequences where each 8-mer occurs 32 times in various positions in the DNA sequence. more...
Organism:
synthetic construct; Mus musculus
Type:
Other
Platforms:
GPL11260 GPL16685
32 Samples
Download data: TXT
Series
Accession:
GSE44338
ID:
200044338
2.

CG methylated microarrays identify novel methylated sequence bound by the CEBPB|ATF4 heterodimer that are active in vivo

(Submitter supplied) To evaluate the effect of CG methylation on DNA binding of sequence-specific B-ZIP transcription factors (TFs) in a high-throughput manner, we enzymatically methylated the cytosine in the CG dinucleotide on protein binding microarrays. Using this novel technology, we show that CG methylation enhanced binding for CEBPA and CEBPB and inhibited binding for CREB, ATF4, JUN, JUND, CEBPD and CEBPG. The CEBPB|ATF4 heterodimer bound a novel motif CGAT|GCAA 10-fold better when methylated. more...
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:
GPL9185 GPL13112
7 Samples
Download data: BED, TXT
Series
Accession:
GSE44942
ID:
200044942
3.

5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) increase CREB1 binding to the C/EBP half-site GCAA

(Submitter supplied) In human and mouse stem cells and brain, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) can occur outside of CG dinucleotides. Using protein binding microarrays (PBMs) containing 60-mer DNA probes, we evaluated the effect of 5mC and 5hmC on one DNA strand on the double-stranded DNA binding of the mouse B-ZIP transcription factors (TFs) CREB1, ATF1, and JUND. 5mC inhibited CREB1 binding to the canonical CRE half-site |GTCA, but increased binding to the C/EBP half-site |GCAA. more...
Organism:
synthetic construct; Mus musculus
Type:
Other
Platform:
GPL11260
18 Samples
Download data: TXT
Series
Accession:
GSE88897
ID:
200088897
4.

Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/enhancer-binding protein beta binding sites

(Submitter supplied) Transcription factors (TFs) bind to thousands of DNA sequences in mammalian genomes, but most of these binding events appear to have no direct effect on gene expression. It is unclear why only a subset of transcription factor bound sites are actively involved in transcriptional regulation, nor are the key genomic features known that discriminate between active and inactive TF binding events. Recent studies have identified promoter-distal RNA polymerase II (RNAP2) binding at enhancer elements, suggesting that these interactions may serve as a potential marker for active regulatory sequences. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL11154
8 Samples
Download data: TXT
5.

Genome-Wide DNA Methylation Profiles in Hematopoietic Stem and Progenitor Cells Reveal Over-Representation of ETS Transcription Factor Binding Sites

(Submitter supplied) DNA methylation is an essential epigenetic mark that is required for normal development. Knockout of the DNA methyltransferase enzymes in the mouse hematopoietic compartment reveals that methylation is critical for hematopoietic differentiation. To better understand the role of DNA methylation in hematopoiesis, we characterized genome-wide DNA methylation in primary mouse hematopoietic stem cells (HSC), common myeloid progenitors (CMP), and erythroblasts (ERY). more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL9185
6 Samples
Download data: BED
Series
Accession:
GSE38354
ID:
200038354
6.

Temporal mapping of C/EBPα and –β binding during liver regeneration

(Submitter supplied) Temporal mapping of C/EBPα and –β binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11002
26 Samples
Download data: BED
Series
Accession:
GSE42321
ID:
200042321
7.

Detection of aberrant DNA methylation in colorectal carcinoma samples compared to normal human colon

(Submitter supplied) To globally define methylation-’prone’ and -’protected’ CpG islands in colorectal carcinoma we analyzed the methylation status of 23,000 CpG islands of the human genome in ten coleorectal carcinoma samples as well as normal colon using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array; Genome variation profiling by genome tiling array
Platform:
GPL8544
10 Samples
Download data: TXT
Series
Accession:
GSE17512
ID:
200017512
8.

Detection of aberrant DNA methylation in acute leukemia samples compared to normal human monocytes

(Submitter supplied) To globally define methylation-’prone’ and -’protected’ CpG islands in leukemia, we analyzed the methylation status of 23,000 CpG islands of the human genome in eight acute leukemia samples as well as normal blood monocytes using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array; Genome variation profiling by genome tiling array
Platform:
GPL8544
8 Samples
Download data: TXT
Series
Accession:
GSE17510
ID:
200017510
9.

Detection of aberrant DNA methylation in AML cell lines compared to normal human monocytes

(Submitter supplied) To globally define methylation-’prone’ and -’protected’ CpG islands in leukemia, we analyzed the methylation status of 23,000 CpG islands of the human genome in two acute leukemia cell lines as well as normal blood monocytes using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL8544
6 Samples
Download data: TXT
Series
Accession:
GSE17455
ID:
200017455
10.

Detection of transcription factor NRF1, YY1 and SP1 bound regions in human peripheral blood monocytes

(Submitter supplied) To study the correlation between sequence motif appearance, transcription factor binding and aberrant hypermethylation in the cell lines, we performed ChIP-on-chip analyses (on CpG island microarrays) for the transcription factors Sp1, NRF1 and YY1 in normal peripheral blood monocytes. Keywords: ChIP-on-Chip; comparative genomic hybridization
Organism:
Homo sapiens
Type:
Genome variation profiling by genome tiling array
Platform:
GPL8544
6 Samples
Download data: TXT
Series
Accession:
GSE16078
ID:
200016078
11.

Transcriptome analysis of myelid cell types (normal and leukemic)

(Submitter supplied) Transcriptome analysis of freshly sorted human CD34+ hematopoietic progenitor cells, human CD14+ peripheral blood monocytes and the human cell line U937 Keywords: one-color based gene expression
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6480
6 Samples
Download data: TXT
Series
Accession:
GSE16076
ID:
200016076
12.

ATF4 Licenses C/EBPb Activity in Human Mesenchymal Stem Cells Primed for Adipogenesis

(Submitter supplied) We report ChIP-seq for C/EBPb and ATF4 in human mesenchymal stem cells and in a cell-free system using naked genomic DNA. ChIP-Seq for GR, RNA Polymerase II, and H3K27 acetylation in hMSCs cultured under different adipogenic conditions are also presented.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL10999 GPL11154 GPL16791
22 Samples
Download data: BED, BEDGRAPH
Series
Accession:
GSE68864
ID:
200068864
13.

ChIp-Chip using RNAP II, CREB C/EBPb and cJun antibody in undifferentiated or differentiated keratinocytes

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by genome tiling array; Expression profiling by array
Platforms:
GPL3793 GPL1261
26 Samples
Download data: CEL, CHP, GFF, PAIR
Series
Accession:
GSE48383
ID:
200048383
14.

ChIp-Chip using RNAP II, CREB C/EBPb and cJun antibody in undifferentiated or differentiated keratinocytes (expression)

(Submitter supplied) Combinatorial recruitment of CREB, C/EBPb and Jun determines activation of promoters upon keratinocyte differentiation Chromatin immunoprecipitation (ChIP) of RNAP II, CREB C/EBPb and cJun in undifferentiated or differentiated keratinocytes demonstrate recruitment of RNAP II to promoters bound by combination of specific transcription factors. Analysis of mRNA expression data from contrl keratinocytes or keratinovtyes where binding of transcription factors is disrupted demonstrate functional requirements for ceratin class of promoters
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
10 Samples
Download data: CEL, CHP
Series
Accession:
GSE48382
ID:
200048382
15.

ChIp-Chip using RNAP II, CREB C/EBPb and cJun antibody in undifferentiated or differentiated keratinocytes (ChIP-Chip)

(Submitter supplied) Combinatorial recruitment of CREB, C/EBPb and Jun determines activation of promoters upon keratinocyte differentiation Chromatin immunoprecipitation (ChIP) of RNAP II, CREB C/EBPb and cJun in undifferentiated or differentiated keratinocytes demonstrate recruitment of RNAP II to promoters bound by combination of specific transcription factors
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL3793
16 Samples
Download data: GFF, PAIR
Series
Accession:
GSE48381
ID:
200048381
16.

Identification of building principles of methylation states at CG rich regions by high-throughput editing of a mammalian genome

(Submitter supplied) Methylation is a repressive modification of DNA prevalent throughout mammalian genomes yet mostly absent at CG rich stretches referred to as CGI. Here we identify their building principles by parallel genomic targeting of sequence libraries. Iterative insertions generated over 3,000 variants of genome-derived and artificial sequences at the same genomic site. Single molecule profiling of the methylation status of this collection allowed modeling the contribution of CG content and DNA binding factors towards the unmethylated state. more...
Organism:
Mus musculus; Escherichia coli; synthetic construct
Type:
Methylation profiling by high throughput sequencing
5 related Platforms
19 Samples
Download data: TXT
Series
Accession:
GSE51170
ID:
200051170
17.

CG hypomethylation in Lsh-/- mouse embryonic fibroblasts is associated with de novo H3K4me1 formation and altered cellular plasticity

(Submitter supplied) DNA methylation patterns are established in early embryogenesis and are critical for cellular differentiation. To investigate the role of CG methylation in potential enhancer formation, we assessed H3K4me1 modification in murine embryonic fibroblasts (MEFs) derived from the DNA methylation mutant Lsh(-/-) mice. We report here de novo formation of putative enhancer elements at CG hypomethylated sites that can be dynamically altered. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL13112 GPL11002
7 Samples
Download data: TXT
Series
Accession:
GSE56151
ID:
200056151
18.

Methylation Profiling of Human Kidney Tubules

(Submitter supplied) We sought to decrease the cell type heterogeneity of kidney tissues to increase the resolution of methylation profiles. To that end, microdissected human kidney tissue from patients are used and hybridized on Illumina HumanMethylation450 BeadChip arrays.
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL13534
85 Samples
Download data: TXT
Series
Accession:
GSE50874
ID:
200050874
19.

Histone tail modification profiles of human renal tubule epithelial cells

(Submitter supplied) To annotate the regulatory elements in the renal tubule epithelial cells, we profiled 6 histone ChIP-seq in the human kidney epithelical cells (HKC8).
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11154
7 Samples
Download data: BED
Series
Accession:
GSE49637
ID:
200049637
20.

Methylation profiles of Human kidney tubules

(Submitter supplied) Epigenetic information in the human kidneys is yet to be studied. In this work, we collected 26 human kidney samples and profiled the genome-wide cytosine methylation patterns using HELP assay.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13223
26 Samples
Download data: PAIR, TXT
Series
Accession:
GSE49557
ID:
200049557
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