Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

40 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PHF6 OCCUPANCYIN HUMAN T-CELL ACUTE LYMPHOBLASTIC LEUKEMIA

ABSTRACT: Here we identify the genome-wide occupancy of PHF6 in 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 PHF6 (Bethyl A301-451A). This represents the ChIP-seq portion of this dataset.

ORGANISM(S): Homo sapiens

SUBMITTER: Richard Young

PROVIDER: E-GEOD-45864 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ChIP-Seq of Histone Methylation and RNAP2 in Human Jurkat cells.

Project description:Three transcriptional states can be defined by histone modifications and RNA polymerase II enriched at promoters and across the body of genes. To gain insight into the active, poised and silent genes in human T-ALL cells, two antibodies against RNAP2, and antibodies against H3K4me3, H3K79me2, and H3K27me3 were used for chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq). Genomic DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against RNAP2, H3K4me3, H3K79me2, and H3K27me3 using whole cell extract (WCE) as a background control. ChIP was performed using a two antibody against hypophosphorylated forms of RNAP2 in two biological replicates. All other ChIPs were done in biological replicates with a single lane of sequencing.

2010-07-24 | E-GEOD-23080 | biostudies-arrayexpress

ChIP-Seq for transcriptional regulators and RNA Polymerase II in tumor cells treated with JQ1

Project description:ChIP-Seq of RNA Polymerase II, and transcriptional regulators in multiple myeloma (MM.1S), glioblastoma (U87-MG), and small cell lung carcinoma (H2171) treated with the BET bromodomain inhibitor JQ1. Cell lines (MM.1S, U87-MG, and H2171) representing multiple myeloma, glioblastoma, and small cell lung carcinoma, were treated with varying concentrations (5nM to 5µM) of the BET bromodomain inhibitor JQ1 followed by ChIP-Seq for RNA Polymerase II and transcriptional regulators. Other datasets from this series of experiments have been release as a part of GSE42355.

2013-07-26 | E-GEOD-49224 | biostudies-arrayexpress

ChIP-Seq of Transcriptional Components in Colon carcinoma

Project description:Discovery of the genome-wide location of proteins using ChIP-Seq has allowed global mapping of the key transcription factors and chromatin regulators that control gene expression programs in various cells. Many DNA-associated processes are targeted for disease therapy. CDK8 is a kinase component of the Mediator co-activator complex and is often over-expressed in colorectal cancer. This study investigates the genome-wide localization of CDK8 in human colorectal cancer cells. Genomic DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against H3K27ac and CDK8 as well as whole-cell extract (WCE) DNA controls.

2013-12-24 | E-GEOD-53602 | biostudies-arrayexpress

cMyc and Max ChIP-seq analysis in small cell lung carcinoma cells

Project description:cMyc and Max ChIP-seq analysis in a high MYC expressing small cell lung carcinoma cell line (H2171) and a low MYC expressing small cell lung carcinoma cell line (H128). H2171 cells (expressing high levels of cMyc protein) and H128 cells (expressing low levels of cMyc protein) were used to analyze how cMyc overexpression influences its genome-wide occupancy.

2012-09-25 | E-GEOD-41105 | biostudies-arrayexpress

ChIP-Seq of transcriptional regulators in MM1S cells upon small molecule treatment.

Project description:Discovery of the genome-wide location of proteins using ChIP-Seq has allowed global mapping of the key transcription factors and chromatin regulators that control gene expression programs in various cells. Many DNA-associated processes are targeted for disease therapy. This study investigates the functions of small molecule therapeutics that target DNA-associated processes involved of CDK9 and BRD4. Genomic DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against RNAP2, BRD4, CDK9, and CTCF using whole cell extract (WCE) as a background control.

2013-04-23 | E-GEOD-43743 | biostudies-arrayexpress

Expression, ChIP-chip, and ChIP-Seq data from REH and SEM leukemia cell lines [ChIP-Seq]

Project description:MLL-fusion proteins are potent inducers of cancer in hematopoietic cells, where they are known to cause changes in global gene expression. How MLL-fusion proteins interact with the genome has not been established, so we have limited understanding of the pathway by which these proteins generate aberrant gene expression programs. Here we describe how the MLL-AF4 protein occupies the genome in human leukemia cells and its striking effects on chromatin states. We find that the MLL-AF4 fusion protein selectively occupies regions of the genome that contain developmental regulatory genes important for hematopoietic stem cell identity and self-renewal. These MLL-AF4 bound regions have grossly altered chromatin structure, with histone modifications catalyzed by Trithorax Group (TrxG) proteins and Dot1 extending across unusually large domains. This indicates that a key feature of MLL-associated leukemogenesis is aberrant targeting of chromatin modifiers to regions of the genome controlling hematopoietic development. Our results define the direct targets of the MLL-fusion protein, reveal the global role of epigenetic misregulation in leukemia, and identify new targets for therapeutic intervention in human cancer. This dataset includes expression data for two replicates each of SEM and REH leukemia cell lines, ChIP-chip data targeting RNAP2, H3K4me3, H3K79me2, ENL, AF4-C, and MLL-N in SEM and REH leukemia cell lines, and ChIP-Seq data of H3K79me2, H3K4me3, ans WCE in SEM and REH cell lines. This Series contains the ChIP-Seq data only. The expression and ChIP-chip data are provided in GEO Series GSE13313.

2012-05-31 | E-GEOD-38338 | biostudies-arrayexpress

Chromatin occupancy of key transcriptional regulators in the presence of the BET bromodomain inhibitor JQ1

Project description:MM1.S cells are an aggressive dexamethasone sensitive multiple myeloma cell line whose transcritional program is driven by deregulated c-Myc activity. We present ChIP-seq analysis of key transcritional regulators that are implicated the c-Myc transcriptional network in MM1.S cells treated with vehicle or 500nM JQ1. Brd4, Cdk9, cMyc, Max, Med1, RNA Pol II, and the chromatin modifications H3K4me3 and H3K27Ac were profiled in MM1.S cells treated with 500nM JQ1 for 24hr

2012-11-30 | E-GEOD-42161 | biostudies-arrayexpress

ChIP-Seq of Transcriptional Components in Ly1 DLBCL and Colon carcinoma

Project description:Discovery of the genome-wide location of proteins using ChIP-Seq has allowed global mapping of the key transcription factors and chromatin regulators that control gene expression programs in various cells. Many DNA-associated processes are targeted for disease therapy. This study investigates the functions of small molecule therapeutics that target DNA-associated processes involved with CDK9 and BRD4. Genomic DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against Brd4, RNA Polymerase II, Med1, H3K27ac, and CDK8 as well as whole-cell extract (WCE) DNA controls

2013-12-24 | E-GEOD-53601 | biostudies-arrayexpress

ChIP-seq of chromatin modifications and factors associated with transcriptionally active regions of the genome in mES cells

Project description:Post-translational modification of histones are coupled to transcription where certain modifications are indicative of an active or inactive region of the genome. Additionally, protein complexes can regulate the placement of nucleosomes across the genome and this influences the ability of DNA-binding proteins to interact with regions of the genome. The datasets presented here are ChIP-seq datasets for chromatin modifications associated with active or poised genes (H2Bub, H3K9,K14Ac and H3K4me3). Brg1 is a subunit of the SWI/SNF chromatin remodeling complex. An antibody specific to the chromatin modification or indicated factor was used to enrich for DNA fragments in murine embryonic stem cells. DNA was purified and prepared for Illumina/Solexa sequencing following their standard protocol.

2012-03-17 | E-GEOD-36561 | biostudies-arrayexpress

ChIP-seq of the HOXA9 and MEIS1 transcription factors in SEM cells.

Project description:SEM cells were established from the peripheral blood of a 5-year-old girl in relapse with acute lymphoblastic leukaemia (ALL). SEM cells exhibit the t(4;11) chromosomal rearrangement, which leads to production of the MLL-AF4 fusion protein. Hematopoietic transcription factors including HOXA9 and MEIS1 are highly expressed in ALL. ChIP-seq was performed against HoxA9 and MEIS1 in SEM cells. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing.

2012-05-31 | E-GEOD-38339 | 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