Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pan-AcH4 ChIP-chip with High Resolution Tiling Arrays on HUVECs and HuAoVSMCs

ABSTRACT: Differential EC enrichment of pan-AcH4 was assessed at 34 select genes, including 19 EC-enriched genes, 6 broadly expressed genes, and 9 EC-excluded genes, by pan-AcH4 (AcH4K5, AcH4K8, AcH4K12, and AcH4K16) ChIP-chip analysis on human umbilical vein endothelial cells (HUVECs) and human aortic vascular smooth muscle cells (HuAoVSMCs) with a high resolution tiling DNA microarray. Specifically, the tiling array analyzes the 50 kb genomic region upstream of transcription initiation, the intragenic regions , and 50 kb genomic region downstream of the last exon.

ORGANISM(S): Homo sapiens

PROVIDER: GSE93962 | GEO | 2018/01/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Pan-AcH3 ChIP-chip with Custom High Resolution Tiling Arrays on HUVECs and HuAoVSMCs

Project description:Differential EC enrichment of pan-AcH3 was assessed at 34 select genes, including 19 EC-enriched genes, 6 broadly expressed genes, and 9 EC-excluded genes, by pan-AcH3 (AcH3K9 and AcH3K14) ChIP-chip analysis on human umbilical vein endothelial cells (HUVECs) and human aortic vascular smooth muscle cells (HuAoVSMCs) with a high resolution tiling DNA microarray. Specifically, the tiling array analyzes the 50 kb genomic region upstream of transcription initiation, the intragenic regions, and 50 kb genomic region downstream of the last exon.

2018-01-19 | GSE93868 | GEO

Tiling path analysis of Drosophila Schneider 2 cultured cells to map forum domains

Project description:Forum domains are stretches of chromosomal DNA that are excised from eukaryotic chromosomes during their spontaneous non-random fragmentation. Mostly forum domains are of 50-200 kb in length, although larger domains, up to 500 - 700 kb, are also observed. <br><br>We performed a genome-wide mapping of forum domains termini in Drosophila Schneider 2 cultured cells using Drosophila melanogaster genomic tiling microarray consisting of overlapping 3 kb fragments. We found that forum domains contain clusters of several or many genes inside. The largest forum domains correspond to the coordinately expressed main clusters of homeotic genes inside BX-C and ANTP-C, cluster of histone genes and clusters of piRNAs. PRE/TRE and binding sites of transcription factors are often reside inside domains, and do not overlap with forum domains termini. The terminal regions of domains often correspond to chromosomal sites containing different classes of mobile elements, binding sites of SuUR protein and regions of intercalary heterochromatin. Our results indicate that forum domains correspond to big multi-gene chromosomal units some of which could be co-coordinately activated or repressed.

2010-11-01 | E-MEXP-2468 | biostudies-arrayexpress

Transcript identification and quantification on Mouse Imprinted Region Tiling Array (MIRTA)

Project description:Transcript identification and quantification on Mouse Imprinted Region Tiling Array (MIRTA)

| PRJNA304313 | ENA

5q21 tiling array on prostate tumors

Project description:CGH profiles of prostate tumors on custom designed high resolution arrays tiling chromosome 5q21 A custom high-density Agilent 15k CGH array tiling 5q21 was designed to narrow down the region of deletion at 5q21 to a few genes that could be followed up with functional studies. 8 critical prostate tumors samples with the most focal regions of deletion were chosen to be profiled on the 5q21 tiling array.

2011-12-19 | E-GEOD-29228 | biostudies-arrayexpress

Systematic analysis of non programmed frameshift suppression in E. coli via translational tiling proteomics

Project description:Programmed ribosomal frameshifting is a process that augments the coding capacity of particular mRNA transcripts. Programmed ribosomal frameshifting may occur during the decoding of chromosomally encoded genes in both prokaryotes and eukaryotes. Although programmed ribosomal frameshifting has been intensively studied, less is known about the occurrence of translation errors that result in frameshifts. Detection of unexpectedly efficient frameshift suppression in E. coli (at levels ranging from 1% to 10% with two unrelated test proteins) led us to investigate the scope of events responsible for restoration of the native frame. To enable a comprehensive approach, we developed a targeted mass-spectrometry method–“translational tiling proteomics”–allowing interrogation of the full set of possible –1 slippage events that could lead to the observed instances of frameshift suppression in vitro and in cells. Our findings point to an unexpectedly high basal level of ribosomal frameshifting, suggest that frameshifted products may contribute more significantly to the proteome than generally assumed, and raise the possibility that particular pseudogenes may specify functional proteins.

2024-01-11 | PXD047675 | Pride

Non-coding RNA tiling array in rice

2007-02-06 | GSE6922 | GEO

Transcriptional Analysis of 1M Regions in Glycine max Using Tiling Microarrays

Project description:We report here a transcriptonal analysis in six different organ types of a approximately 1 Mb region in soybean (Glycine max) which is sytenic with legume (Medicago truncatula). We used oligonucleotide tiling microarrays to detecte transcription of over 80% of the predicted genes in both species. We detected differential gene expression in the six examined organ types. Keywords: RNA

2008-01-15 | GSE10056 | GEO

Transcriptional Analysis of 1M Regions in Medicago truncatula Using Tiling Microarrays

Project description:We report here a transcriptonal analysis in six different organ types of a approximately 1 Mb region in legume plants barrel medic (Medicago truncatula) which is sytenic with soybean (Glycine max). We used oligonucleotide tiling microarrays to detecte transcription of over 80% of the predicted genes in both species. We detected differential gene expression in the six examined organ types. Keywords: RNA

2008-01-15 | GSE10055 | GEO

Comparison of HBO1 siRNA-treated Human Umbilical Vein Endothelial Cells (HUVECs) and control siRNA-treated HUVECs

Project description:To determine the role of HBO1 in EC physiology, gene expression analysis was conducted on control and HBO1 siRNA-treated HUVECs. A total of 263 differentially regulated protein-coding transcripts were detected, many of which are key for growth and angiogenesis. Additionally, many genes involved in cell cycle, cell division, and DNA replication were dysregulated. HBO1-regulated genes were verified by qRT-PCR, including those with roles in vessel tone regulation (e.g. ACE1), vessel formation (e.g. CXCL16), EC activation (e.g. E-selectin), and cholesterol efflux (e.g. ABCG1).

2018-01-19 | GSE93608 | GEO

Non-coding RNA tiling array in rice

Project description:The 1 Mb tiling array was used to represent the 10.0 Mb to 11.0 Mb region of japonica rice Chromosome 10. A tile path was designed with 36-mer probes at a step of 5 nt. All 388,994 probes were retained and synthesized into a single array. This array was hybridized to the cDNA target used for the full-genome tiling array as well as targets prepared from non-coding RNA sample I and II. Keywords: noncoding RNA Non-coding RNA species were isolated from total RNA as previously described (5). Briefly, total RNA isolated from japonica rice leaves using the Trizol method was loaded onto an Qiagen-tip and eluted with 0.6~1.0M NaCl gradient of QRW2 buffer (Qiagen) at 50 oC. Fractions corresponding to tRNAs (sample I) and small RNAs of 80-500 nucleotides (nt) (sample II) were collected. To remove remaining mRNAs and rRNAs, the small RNA fractions were hybridized to a mixture of specifically designed oligos in the binding buffer. Unwanted RNA molecules were targeted and removed by a magnetic bead based process (MicrobExpress kit, Ambion). The enriched non-coding RNA pool was then dephosphorylated with a calf intestine alkaline phosphatase and ligated to a 3ï¢ adaptor oligonucleotide by the T4 RNA ligase (5). Small size molecules and excessive adaptors were removed from the ligation products using the mirVana miRNA isolation kit (Ambion) and reverse transcribed at 50 oC using the Thermoscript (Invitrogen) and the oligo 3RT as the primer (5). Amino-allyl-modified dCTP was incorporated into the cDNA strand during reverse transcription.

2010-06-11 | E-GEOD-6922 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data