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Series GSE52553 Query DataSets for GSE52553
Status Public on Oct 22, 2014
Title Ethanol treatment of lymphoblastoid cell lines from alcoholics and non-alcoholics causes many subtle changes in gene expression
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Compared gene expression in lymphoblasoid cell lines from alcholics and controls and 24 hr treatment with ethanol.
To elucidate the effects of a controlled exposure to ethanol on gene expression, we studied lymphoblastoid cell lines (LCLs) from 21 alcoholics and 21 controls. We cultured each cell line for 24 h with and without 75 mM ethanol and measured gene expression using microarrays. Differences in expression between LCL from alcoholics and controls were modest, but included 13 genes previously identified as associated with alcoholism or related traits in one or more GWAS, including KCNA3, DICER1, ZNF415, Catalase and PPARGC1B. The paired design allowed us to detect very small changes due to ethanol treatment: ethanol altered the expression of 37% of the probe sets (51% of the unique named genes) detectably expressed in these LCLs, but most by very modest amounts. 99% of the named genes expressed in the LCLs were also expressed in at least 1 of 9 brain regions tested, suggesting that LCLs are a reasonable and accessible proxy for brain tissues. Key pathways affected by ethanol include cytokine, TNF and NF-kB signaling. Among the genes affected by ethanol were ANK3, EPHB1, SLC1A1, SLC9A9, NRD1, and SH3BP5, which were reported to be associated with alcoholism or related phenotypes in 2 genome wide association studies. Genes that either differed in expression between alcoholics and controls or were affected by ethanol exposure are candidates for further study.
 
Overall design Lymphoblastoid cells from 21 alcoholics and 21 controls were treated with 75mM ethanol for 24 hours.
 
Contributor(s) McClintick JN, Tischfield JA, Edenberg HJ
Citation(s) 25129674
Submission date Nov 20, 2013
Last update date Mar 25, 2019
Contact name Jeanette Nance McClintick
E-mail(s) jnmcclin@iu.edu
Organization name Indiana University School of Medicine
Department Biochemistry & Molecular Biology
Lab Center for Medical Genomics
Street address 635 Barnhill Dr.
City Indianapolis
State/province IN
ZIP/Postal code 46202
Country USA
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (84)
GSM1269644 F_Alcoholic_37_None
GSM1269645 F_Alcoholic_37_ethanol
GSM1269646 M_Alcoholic_27_None
Relations
BioProject PRJNA229371

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
GSE52553_RAW.tar 432.6 Mb (http)(custom) TAR (of CEL, CHP)
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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