Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

H4IIE liver cell line ChIP-Chip with Egr1

ABSTRACT: Egr1 regulates genes involved in cholesterol biosynthesis in liver. ChIP-chip assays were performed on H4IIE liver cells that were either treated or untreated with insulin for one hour. This experiment includes a custom ChIP-chip design incorporating many genes that are dynamically regulated by insulin signaling. The Egr1 antibody used was from Santa Cruz sc-189.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE30823 | GEO | 2011/07/23

SECONDARY ACCESSION(S): PRJNA144193

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

H4IIE liver cell line ChIP-Chip with Egr1

Project description:Egr1 regulates genes involved in cholesterol biosynthesis in liver. ChIP-chip assays were performed on H4IIE liver cells that were either treated or untreated with insulin for one hour. This experiment includes a custom ChIP-chip design incorporating many genes that are dynamically regulated by insulin signaling. The Egr1 antibody used was from Santa Cruz sc-189. Egr1 ChIP samples from untreated and 1h insulin treated cells were hybridized.

2011-07-22 | E-GEOD-30823 | biostudies-arrayexpress

P15 Rat Sciatic Nerve ChIP-Chip with NuRD complex components

Project description:The NuRD complex is required for efficient and timely myelination in the peripheral nervous system. ChIP-chip assays were performed on rat sciatic nerve at P15, a peak timepoint of myelination, for binding of Chd4 to genes involved in regulating myelin formation. This experiment includes two custom ChIP-chip design incorporating many genes that are dynamically regulated during myelination. The antibodies used in this platform were Chd3/4 (Santa Cruz sc-11378) Chd4 (gift from Paul Wade), Mta2 (Santa Cruz sc-9447), and Nab2 (Santa Cruz sc-22815).

2011-07-26 | GSE30890 | GEO

P15 Rat Sciatic Nerve ChIP-Chip with NuRD complex components

2011-07-25 | E-GEOD-30890 | biostudies-arrayexpress

Mapping of cohesin, CTCF and a collection of tissue-specific and ubiquitous transcriptional regulators using ChIP-seq in primary wild type and Rad21-cohesin haploinsufficient mouse liver

Project description:Mapping of cohesin, CTCF and a collection of tissue-specific and ubiquitous transcriptional regulators using ChIP-seq in primary mouse liver. The following antibodies were used: CTCF (upstate, 07729), STAG1 (abcam, ab4457), STAG2 (abcam, 4464), RAD21 (abcam, ab992), CEBPA (santa cruz, sc9314), HNF4A (aviva systems biology, ARP31946), FOXA1 (abcam, ab5089), FOXA2 (santa cruz, sc6554), HNF6 (santa cruz, sc13050), HNF1A (santa cruz, sc6547), PREP1 (santa cruz, sc6245), NRSF/REST (santa cruz, sc25398), GABPA (santa cruz, sc22810), E2F4 (santa cruz, sc1082), p300 (santa cruz, sc585), CBP (santa cruz, sc369), RNAP2 (abcam, ab5408), H3K4me1 (abcam, ab8895), H3K4me3 (abcam, ab8580), H3K36me3 (abcam, ab9050), H3K79me2 (abcam, ab3594), H2AK5ac (abcam, 1764)

2012-06-22 | E-MTAB-941 | biostudies-arrayexpress

Identification of ChIP-seq and RIME grade antibodies for Estrogen Receptor alpha

Project description:Estrogen Receptor alpha (ERα) is a key driver of most breast cancers, and it is the target of endocrine therapies used in the clinic to treat women with ERα positive (ER+) breast cancer. The two methods ChIP-seq (chromatin immunoprecipitation coupled with deep sequencing) and RIME (Rapid Immunoprecipitation of Endogenous Proteins) have greatly improved our understanding of ERα function during breast cancer progression and in response to anti-estrogens. A critical component of both ChIP-seq and RIME protocols is the antibody that is used to pull down the bait protein. To date, most of the ChIP-seq and RIME experiments for the study of ERα have been performed using the sc-543 antibody from Santa Cruz Biotechnology. However, this antibody has been discontinued, thereby severely impacting the study of ERα in normal physiology as well as diseases such as breast cancer and ovarian cancer. Here, we compare the sc-543 antibody with other commercially available antibodies, and we show that 06-935 (EMD Millipore) and ab3575 (Abcam) antibodies can successfully replace the sc-543 antibody for ChIP-seq and RIME experiments.

2019-03-21 | PXD012930 | Pride

Egr1 regulates the coordinated expression of numerous EGF receptor target genes as identified by ChIP-on-chip

Project description:Previous studies have revealed that UV-stimulation of a variety of cells leads to activation of the EGF receptor, induction of Egr1, growth inhibition and apoptosis. On the other hand both Egr1 and EGF receptor activation are implicated in promoting the progression of prostate cancer. We treated M12 tumorigenic prostate epithelial cells which express little Egr1 with UV irradiation which rapidly activated the EGF receptor and elevated Egr1. Treatment with specific EGFR and ERKI/II inhibitors (PD153035 and UO126, respectively) confirmed that the upregulation of Egr1 was downstream of EGFR and ERKI/II Map kinase pathway. ChIP on chip experiments using Egr1 antibody identified 288 significantly bound promoters upon UV stimulation. Of these target genes, 40% had consensus Egr1 site in their promoters, considerably greater than that expected by chance (p < 0.005). The array binding results were validated by PCR analysis of 25 genes using DNA from conventional IP experiment. Affymetrix gene expression analysis of UV treated and control cells confirmed that a significant number of these bound promoters showed gene expression changes. Addition of siRNA to Egr1 confirmed that the gene expression changes were dependent upon Egr1 expression. Addition of EGF led to similar expression changes for nine tested genes. Proliferation and apoptosis assays confirmed that M12 cells undergo growth arrest and apoptosis following UV irradiation. Moreover, addition of EGF also promoted significant growth inhibition. These results indicate the M12 cells undergo a EGF receptor dependent apoptosis response upon UV-stimulation and that Egr1 mediates the regulation of numerous genes downstream of the EGF receptor that are associated with this response. Keywords: UV treatment analysis duplicated experiment for Affymetrix gene expression analysis and Chip-on-Chip analysis.

2010-05-06 | E-GEOD-10585 | biostudies-arrayexpress

[E-TABM-828] ChIP-Seq in human MCF7 and HEPG2 cells

Project description:ChIP-Seq study in human MCF7 and HEPG2 cells using antibodies against CTCF (Millipore, 07-729), STAG1 (abcam, ab4457), RAD21 (abcam, ab992), ERa (santa cruz, sc-543), CEBPa (santa cruz, sc-9314) ArrayExpress Release Date: 2010-05-12 Publication Title: A CTCF-independent role for cohesin in tissue-specific transcription Publication Author List: Dominic Schmidt, Petra C. Schwalie, Caryn S. Ross-Innes, Antoni Hurtado, Gordon D. Brown, Jason S. Carroll, Paul Flicek and Duncan T. Odom Person Roles: submitter Person Last Name: Schwalie Person First Name: Petra Catalina Person Email: schwalie@ebi.ac.uk Person Address: Person Affiliation: EBI

2011-02-05 | GSE25021 | GEO

ChIP-Seq of TAL1 and its regulatory partners in T-ALL cells

Project description:The oncogenic transcription factor TAL1/SCL is aberrantly expressed in over 40% of cases of T-cell acute lymphoblastic leukemia (T-ALL), emphasizing its importance in the molecular pathogenesis of T-ALL. Here we identify the core transcriptional regulatory circuit controlled by TAL1 and its regulatory partners HEB, E2A, LMO1, LMO2, GATA3 and RUNX1 in T-ALL cells. We show that TAL1 forms an interconnected auto-regulatory loop with its partners, and that the TAL1 complex directly activates the MYB oncogene, forming a feed-forward positive regulatory loop that further promotes the TAL1-regulated oncogenic program. one of the cirtical downstream targets in this circuitry is the TRIB2 gene, which is oppositely regulated by TAL1 and HEB/E2A, and is essential for the survival of T-ALL cells. Human T-ALL cells were cross-linked with formaldehyde for 20 min. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against total TAL1 (Santa Cruz SC-12984), TCF12/HEB (Santa Cruz SC-357),TCF3/E2A (Santa Cruz SC-349X), LMO1 (Santa Cruz SC-10494), LMO2 (R&D AF2726),GATA3 (Santa Cruz SC-22206) and RUNX1 (Santa Cruz SC-8563). This represents the ChIP-seq portion of this dataset.

2012-02-09 | E-GEOD-29180 | biostudies-arrayexpress

ChIP-Seq of human MCF7 and HEPG2 cells using antibodies against CTCF, STAG1, RAD2, ERa and CEBPa

2010-05-13 | E-TABM-828 | biostudies-arrayexpress

EGR1 ChIP-seq targeted to Npy and its receptors

Project description:We used ChIP-seq to identify possible EGR1 (Early growth response 1) binding sites in Npy, Npy1/2/5/r in the dorso-lateral striatum in C57BL/6J mice.

2017-03-30 | E-MTAB-5503 | 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