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Series GSE56069 Query DataSets for GSE56069
Status Public on Mar 24, 2015
Title Immortalization of T-cells is accompanied by gradual changes in CpG methylation resulting in a profile resembling a subset of T-cell leukemias [expression]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary We have previously described gene expression changes during spontaneous immortalization of T cells, thereby identifying cellular processes important for cell growth crisis escape and long term proliferation. Here we analyze the same model to investigate the role of genome-wide methylation in the immortalization process at different time points pre- and post- crisis using high-resolution arrays. We show that over time in culture there is an overall accumulation of methylation alterations, with preferential increased methylation close to transcription start sites, island and shore regions. Most methylation alterations did not affect gene expression but among the affected genes, increased methylation close to transcription start site was associated with decreased gene expression. Interestingly, the pattern of CpG site methylation observed in post-crisis T-cell cultures was similar to clinical T-cell acute lymphoblastic leukemia (T-ALL) samples classified as CpG island methylator phenotype positive (CIMP+). These sites were highly overrepresented by polycomb target genes and involved in developmental, cell adhesion and cell signaling processes. The presence of nonrandom methylation events in in vitro immortalized T-cell cultures and diagnostic T-ALL samples indicates altered methylation of CpG sites with a possible role in malignant hematopoiesis.
Overall design RNA was extracted with TRIZOL according to manufacturer instructions. Total RNA was amplified bu the Illumina TotalPrep RNA Amplification kit.
Gene expression array analysis was performed on the cell cultures.
Contributor(s) Degerman S, Landfors M, Siwicki JK, Revie J, Borssén M, Evelönn E, Forestier E, Chrzanowska KH, Rydén P, Keith WN, Roos G
Citation(s) 25065939
Submission date Mar 20, 2014
Last update date Aug 16, 2018
Contact name Sofie Degerman
Organization name Umeå University
Department Medical Biosciensces
Lab Pathology
Street address NUS, Blg 6M, 2nd floor
City Umeå
State/province Sweden
ZIP/Postal code 90185
Country Sweden
Platforms (1)
GPL6947 Illumina HumanHT-12 V3.0 expression beadchip
Samples (9)
GSM1354606 total RNA from S3R 17 PD
GSM1354607 total RNA from S3R 27 PD
GSM1354608 total RNA from S3R 76 PD
This SubSeries is part of SuperSeries:
GSE56070 Immortalization of T-cells is accompanied by gradual changes in CpG methylation resulting in a profile resembling a subset of T-cell leukemias
BioProject PRJNA242335

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
GSE56069_RAW.tar 6.2 Mb (http)(custom) TAR
GSE56069_non_normalized.txt.gz 2.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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