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Series GSE126904 Query DataSets for GSE126904
Status Public on Feb 22, 2019
Title TNFα and LTβ stimulated UM-SCC 46 gene expression [TNF]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary To investigate the regulatory mechanisms and targets of the activation of NF-kB and inflammatory pathways, we treated HPV(-) head and neck cancer line UM-SCC 46 cells with TNFα and LTβ at different time points, and compared the gene expression by microarray. TNFα uniquely induced 172 genes, LTβ specifically induced 202 genes, while 155 genes were induced by both ligands.
Total RNA samples were isolated from UM-SCC 46 cells after TNFα or LTβ treatment at different time points, and the gene expression were compared with untreated cell controls.
 
Overall design UM-SCC 46 cells were treated with TNFα (20ng/ml) or LTβ (100ng/ml) for 1, 3, 6, 12, and 24 hours. RNA was isolated and global gene expression was examined by beads based array using Illumina HumanWG-6-v3-BeadChip (Illumina, CA). Raw data were imported to the GenomeStudio software, and normalized data were imported to Parte to detect differentially expressed genes by using an ANOVA test. Hierarchical clustering of altered gene expression when treated with LTβ was compared to untreated cells using MeV software. The heat map represents two-fold increased gene expression when compared to untreated samples.
 
Contributor(s) Yang X, Cheng T, Chen Z
Citation(s) 30488488
Submission date Feb 21, 2019
Last update date May 24, 2019
Contact name Carter Van Waes
E-mail(s) vanwaesc@nidcd.nih.gov
Phone 301-402-4216
Organization name NIDCD
Department Head and Neck Surgery Branch
Street address 10 Center Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (1)
GPL18387 Illumina HumanWG-6 v3.0 expression beadchip (gene symbol)
Samples (6)
GSM3618008 UM-SCC46_noTreat_0hr_for_TNF
GSM3618009 UM-SCC46_TNFa_1hr
GSM3618010 UM-SCC46_TNFa_3hr
This SubSeries is part of SuperSeries:
GSE126905 TNFa and LTB stimulated UM-SCC 46 gene expression
Relations
BioProject PRJNA523626

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE126904_RAW.tar 13.2 Mb (http)(custom) TAR (of IDAT)
GSE126904_UMSCC46_TNF_normalized.xlsx 2.4 Mb (ftp)(http) XLSX
Processed data included within Sample table
Processed data are available on Series record

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