Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Combinatorial transcription factor binding evolution in five placental mammals

ABSTRACT: Zoo-ChIP: Functional analysis of experimentally determined combinatorial transcription factor binding in multiple mammalian species

INSTRUMENT(S): Illumina Genome Analyzer II

ORGANISM(S): Rattus norvegicus

SUBMITTER: Michael Wilson

PROVIDER: E-MTAB-1509 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

A CpG mutational hotspot in a ONECUT (HNF6) binding site accounts for the prevalent variant of Hemophilia B Leyden

Project description:Hemophilia B, or the 'Royal Disease', arises from mutations in the Coagulation Factor IX (F9) gene. Mutations within the F9 promoter are associated with a remarkable form of the disease, termed Hemophilia B Leyden, in which symptoms ameliorate after puberty. Mutations at the -5/-6 site account for the majority of Leyden cases, and have been postulated to disrupt the binding of a transcriptional activator, the identity of which has remained elusive for more than twenty years. Here we show that the ONECUT transcription factors (ONECUT1/HNF6 and ONECUT2/HNF6B) bind to the -5/-6 site. The various Hemophilia B Leyden mutations that have been reported in this site inhibit ONECUT binding to varying degrees that correlate well with their associated clinical severities. In addition, expression of F9 is crucially dependent on ONECUT factors in vivo and as such, mice that are deficient in either ONECUT1, ONECUT2 or both, exhibit depleted levels of F9. Taken together, our findings establish the ONECUT transcription factors as the missing regulators of Hemophilia B Leyden that operate through the -5/-6 site.

2013-03-06 | E-MTAB-890 | biostudies-arrayexpress

Mapping ONECUT1 TF binding with ChIP-exo

Project description:The aim of this project is to locate the precise binding of the ONECUT1 transcription factor. NOTE: This study was updated on 7th May 2014. All samples, experiments, runs and files were replaced. This was due to an incorrect reagent being used in the earlier version.

2014-05-10 | E-MTAB-2060 | biostudies-arrayexpress

Epigenetic comparison of human DNA in specific human tissues to human DNA in transgenic mouse tissues

Project description:This project aims to study human repetitive elements on human chromosome 21 (HsChr21) in a heterologous mouse environment (Tc1 mouse). The in vivo, HsChr21-wide enrichment of active histone modified regions (H3K4me3) and transcription factor binding sites was profiled by ChIP-seq in Human and Tc1 mouse tissue in order to determine the unbiased regulation of the human genome.

2013-03-21 | E-MTAB-1104 | biostudies-arrayexpress

Genomic localization of Topoisomerase II beta

Project description:ChIP-seq of Top2b, CTCF, Rad21, H3K4me2, H3K36me3 in mouse liver. ChIP-exo of CTCF, Rad21 and Top2b

2016-08-05 | E-MTAB-3587 | biostudies-arrayexpress

Genome-wide mapping of SPDEF and ESR1 binding in MCF-7 cells (ChIP-seq)

Project description:Using a transcriptional network derived from 2000 breast cancer gene expression profiles we identify the master regulators (MRs) of FGFR2 signalling. To validate the identified regulons, we examined whether there was enrichment of TF binding near the transcription start sites (TSS) of genes found in the regulons of a particular MR. For ESR1 and SPDEF, ChIP-seq experiments were performed in MCF-7 cells, while existing data was analysed for FOXA1 (Hurtado et al. Nature Genetics, 43:27–33, 2010) and GATA3 (Theodorou, et al., Genome Res 23: 12-22, 2013). ChIP-seq experiments were performed on three biological replicates per each transcription factor. For each sample, 36bp single-end reads were obtained. Peak regions were identified in all ChIP-seq TF data sets using the peak caller algorithm MACS (Zhang et al., Genome Biology, 9(9):R137, 2008) with default parameters.

2013-07-17 | E-GEOD-48930 | biostudies-arrayexpress

Carroll_ChIP_exo

Project description:This experiment validates the ChIP-exo protocol on the Illumina sequencing platform.

2014-01-15 | E-MTAB-1827 | biostudies-arrayexpress

Chromatin immunoprecipitation of TCF4 in human LS174AT cells using Nimblegen human genome-wide chips

Project description:genome-wide ChIP-on-chip against TCF4 in LS174T cells, performed on NimbleGen Systems, Inc. human genome-wide 38-chip, hg17 array set followed by verification using biological replicates on a dedicated design.

2008-02-13 | E-TABM-402 | biostudies-arrayexpress

Exploration of the redundancy between FOXA1 and AP2alpha in androgen receptor transcription complex

Project description:We performed a comparision of AR binding sites as well as the histone modifications H3K27 acetylation and H3K4 monomethylation in the presence and absence of FoxA1 in the molecular apocrine breast cancer cell line, MDA-MB-453. We also probed AP2alpha binding in asynchronous MDA-MB-453 cells.

2014-04-17 | E-MTAB-1694 | biostudies-arrayexpress

Effect of FOXA1 over-expression upon AR binding in AR-driven cancers

Project description:We performed androgen receptor (AR) ChIP-seq after GFP control or FOXA1 over-expression in two AR driven cancer models; LNCaP prostate cancer cell line and MDA-MB-453 molecular apocrine breast cancer cell line.

2014-01-14 | E-MTAB-1749 | biostudies-arrayexpress

ChiP-seq profiling of Drosophila melanogaster salivary glands to identify targets for NSL1 and MCRS2.

Project description:ChiP-seq profiling of Drosophila melanogaster salivary glands to identify targets for NSL1 and MCRS2.

2010-06-25 | E-MTAB-214 | biostudies-arrayexpress