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Series GSE134396 Query DataSets for GSE134396
Status Public on Jul 18, 2019
Title Paradoxical association of TET loss of function with genome-wide hypomethylation
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Other
Expression profiling by high throughput sequencing
Summary Cancer genomes are characterized by focal increases in DNA methylation, co-occurring with widespread hypomethylation. Here we show that TET loss-of-function results in a similar genomic footprint. Both 5hmC in wildtype genomes, and DNA hypermethylation in TET-deficient genomes, are largely confined to the active euchromatic compartment, consistent with the known functions of TET proteins in DNA demethylation and the known distribution of 5hmC at transcribed genes and active enhancers. In contrast, an unexpected DNA hypomethylation noted in multiple TET-deficient genomes is primarily observed in the heterochromatin compartment. In a mouse model of T cell lymphoma driven by TET deficiency (Tet2/3 DKO T cells), genomic analysis of malignant T cells revealed DNA hypomethylation in the heterochromatic genomic compartment, as well as reactivation of repeat elements and enrichment for single nucleotide alterations, primarily in heterochromatic regions of the genome.
 
Overall design WGBS (MethylC-seq), Hi-C, and total (ribodepleted) RNA-seq, in WT and Tet2/3 DKO iNKT cells
 
Contributor(s) López-Moyado IF, Tsagaratou A, Seo H, Delatte B, Heinz S, Benner C
Citation(s) 31371502
Submission date Jul 17, 2019
Last update date Aug 05, 2019
Contact name Isaac F. López-Moyado
E-mail(s) ilopezmo@eng.ucsd.edu
Organization name La Jolla Institute for Immunology
Department Division of Signaling and Gene Expression
Lab Anjana Rao's laboratory
Street address 9420 Athena Cir
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (11)
GSM3945715 WGBS (MethylC-seq) Tet2/3 DKO iNKT transferred and expanded Biol. Rep. 1
GSM3945716 WGBS (MethylC-seq) Tet2/3 DKO iNKT transferred and expanded Biol. Rep. 2
GSM3945717 Hi-C WT iNKT thymus
Relations
BioProject PRJNA555063
SRA SRP215028

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
GSE134396_NKT_ribofree.cntTable.txt.gz 139.1 Kb (ftp)(http) TXT
GSE134396_RAW.tar 235.2 Mb (http)(custom) TAR (of BEDGRAPH, TXT)
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Processed data provided as supplementary file
Raw data are available in SRA
Processed data are available on Series record

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