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Title: Expression profiling by array in ATLL      
dateReleased:
05-16-2013
description:
Previously, we have shown that an AP-1 family member Fra-2, which is hardly expressed in normal mature T cells, is consistently over-expressed in adult T-cell leukemia/lymphoma (ATLL), and together with JunD, upregulates CCR4 and many other genes including proto-oncogenes c-Myb, MDM2, Bcl-6, and SOX4. SOX4 is frequently overexpressed in many solid tumors and considered to be a potential oncogene. To identify downstream target genes of SOX4 and analyze SOX4 oncogenic pathway in ATLL , we compared gene expression profiles of ST1 cells transfected with SOX4 siRNA or control siRNA using the Affymetrix high density oligonucleotide microarray. The ATL-derived cell line ST1 was transfected with control siRNA or SOX4 siRNA using Nucleofector® (Lonza, Basel, Switzerland). To determine the high-viability of the cells transfected with siRNAs, the cells were counted after 6 h on FACSCalibur (Becton Dickinson, Mountain View, CA) by gating out cells stained with propidium iodide. The transfection efficiency of RNAs was close to 95%, as determined by using fluorescent siRNA (Qiagen). After 48 h, total RNA samples were prepared and confirmed to be of good quality with the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). In addition, quantitative PCR confirmed that SOX4 siRNA effectively reduced SOX4 mRNA in ST1 cells.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-38021
refinement:
raw
alternateIdentifiers:
38021
keywords:
functional genomics
dateModified:
06-02-2014
availability:
available
types:
gene expression
name:
Homo sapiens
ID:
A-AFFY-44
name:
Affymetrix GeneChip Human Genome U133 Plus 2.0 [HG-U133_Plus_2]
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-38021/E-GEOD-38021.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-38021/E-GEOD-38021.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38021
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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