Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An integrated functional genomics approach identifies the regulatory network directed by brachyury in chordoma

ABSTRACT: shRNA-mediated brachyury knockdown was performed on the chordoma cell line U-CH1 as replicates. RNA was extracted, labelled and hybridised to Human Gene 1.0ST chips followed by gene expression microarray analysis.This was followed by a ChIP-seq experiment using a specific brachyury antibody, the data for which are stored in Raw ChIP-seq reads are stored under: European Nucleotide Archive accession ERP000953 and Array Express accession E-ERAD-23.

ORGANISM(S): Homo sapiens

SUBMITTER: Nischalan Pillay

PROVIDER: E-MEXP-3716 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

A common single nucleotide variant in T is strongly associated with chordoma

Project description:Gene expression profile of human chordoma samples. These samples were combined with the chordoma samples from those of E-MEXP-353. These were normalised and batch corrected as per materials and methods in the published paper. Gene set enrichment analysis was then performed to determine enrichment of target genes of T between the rs2305089 genotypes (GA vs AA).

2013-08-20 | E-MEXP-3717 | biostudies-arrayexpress

Sumoylation at Chromatin Governs Coordinated Repression of a Transcriptionnal Program Essential for Cell Growth and Proliferation 2

Project description:mRNA profiling of proliferative versus Ras-induced senescent human primary fibroblasts 5 days post-infection. The goals of this study is to analyse transcriptional changes in senescent cells (RASv12 infected cells)

2013-11-25 | E-MEXP-3777 | biostudies-arrayexpress

transcriptome analysis of SIRT2 dependent genes modulated during infection by Listeria monocytogenes

Project description:tissue culture cells were treated with an inhibitor to the deacetylase SIRT2 (AGK2) and infected with Listeria monocytogenes

2013-06-01 | E-MEXP-3912 | biostudies-arrayexpress

Integrated analysis of copy number variation and genome-wide expression profiling in colorectal cancer using macrodissected tissues

Project description:The experiment was to elucidate the association between copy number variation (CNV) and gene expression in colorectal cancer (CRC) samples and their corresponding non-cancerous tissues.

2014-06-30 | E-MEXP-3980 | biostudies-arrayexpress

Follicular B (FoB) cells purified from miR-17-92 transgenic mice

Project description:We have generated a miR-17-92 transgenic allele (termed miR-17-92 Tg) whose expression can be turned on conditionally by Cre recombinase (Xiao et al, Nature Immunology, 9:405-14, 2008). The mice were crossed to CD19-Cre mice to turn on the transgene expression specifically in B cells. Follicular B(FoB) cells were purified from CD19-Cre;miR-17~92 Tg/Tg mice (FoBtg1, FoBtg2, FoBtg3) and miR-17~92 Tg/Tg mice (FoBwt1, FoBwt2, FoBwt3) by MACS depletion of cells positive for CD5, CD43, and CD93 (also known as AA4.1). The purity of follicular B cells was examined by flow cytometry and was greater than 95% for all samples. Total RNA was extracted using RNeasy kit (QIAGEN).

2011-07-21 | E-GEOD-30877 | biostudies-arrayexpress

Transcription profile of dendritic cell line D1 treated with Lactococcus Lactis

Project description:Effect of Lactococcuc Lactis (MOI 1:1000) on D1 dendritic cells on different time points: 0h, 4h, 8h, 24h

2012-03-28 | E-MEXP-3162 | biostudies-arrayexpress

Transcriptome of M. tuberculosis-infected human macrophages in the presence of ATP

Project description:Human monocyte-derived macrophages were infected with Mycobacterium tuberculosis (H37Rv strain) at a multiplicity of infection 1:1. After 2h of incubation, cells were washed to remove extracellular bacteria and were incubated in fresh medium for a further 18h in the presence or not of 100microM ATP. Total RNA was then extracted and gene expression was determined using HuGene 1.0 ST microarrays (Affymetrix, Inc.,Santa Clara, CA).

2013-06-01 | E-MEXP-3805 | biostudies-arrayexpress

Expression data from five primary human glioblastomas (frozen surgical resection) and one non-neoplastic adult brain (frozen autopsy tissue)

Project description:DNA hypomethylation could lead to activation of alternate promoters in GBM. We profiled DNA methylation and H3K4me3 genome-wide, and also performed expression and copy number analysis on the same samples In this dataset, we include all expression data obtained for five GBMs and one normal brain. We identified loci with concurrent DNA hypomethylation and H3K4me3 in GBM, and analyzed expression of the nearest gene in the same sample using these data Six total samples were analyzed. Each GBM sample was compared to normal brain to obtain expression changes

2013-08-13 | E-GEOD-49412 | biostudies-arrayexpress

Spinophilin silencing in the breast cancer cell line SUM159

Project description:Microarray profiling was used to determine the most abundantly expressed genes in spinophilin-silenced breast cancer cells compared to control cells in the cell line SUM159. We identified several differentially expressed genes in spinophilin-silenced cells. A total number of six samples were analyzed, each in three replicates. There are three SUM159 Control samples and three samples of the cell line SUM159 with silenced spinophilin.

2014-10-01 | E-GEOD-61889 | biostudies-arrayexpress

Clinical drug resistance linked to inter-convertible phenotypic and functional states of tumor-propagating cells in multiple myeloma

Project description:To gain insights into the molecular mechanisms underpinning the reversible, bi-directional CD138- Pre-PC and CD138+ PC transition we subjected highly purified (>99%) Pre-PC - PC pairs from 9 patients to global mRNA expression profiling

2012-11-21 | E-MEXP-3772 | 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