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Series GSE173344 Query DataSets for GSE173344
Status Public on Oct 26, 2021
Title TET2-mediated deprogramming of breast cancer cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Methylation and demethylation of cytosines in DNA are believed to act as keystones of cell-specific gene expression through controlling chromatin structure and accessibility to transcription factors. Cancer cells have their own transcriptional programs and we sought to alter such a cancer-specific program by enforcing expression of the catalytic domain (CD) of the methylcytosine dioxygenase TET2 in breast cancer cells. TET2 CD decreased the tumorigenic potential of cancer cells through both activation and repression of a repertoire of genes. In addition to promoting the establishment of an antiviral state, TET2 activated 5mC turnover at thousands of MYC binding motifs and down-regulated a panel of known MYC-repressed genes involved in lysosome biogenesis and function.
Overall design MCF-7 cells stably transfected with an empty vector or with plasmids encoding either wild type mouse TET2 catalytic domain (CD - aa916-1921, pcDNA3-Flag-TET2 CD, addgene #72219) or the catalytically dead mutant H1304Y, D1306A mutant (pcDNA3-Flag-TET2 mCD, addgene #72220) were analyzed for gene expression by RNA-seq and for chromatin marks by ChIP-seq (H3K4me3 and H3K27me3) and selective chemical labeling (5hmC).
Contributor(s) Salbert G, Avner S
Citation(s) 35351824
Submission date Apr 26, 2021
Last update date Apr 20, 2022
Contact name Gilles Salbert
Organization name University Rennes 1
Department IGDR UMR6290
Street address 263 Av. Gal. Leclerc
City Rennes
ZIP/Postal code 35200
Country France
Platforms (3)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (63)
GSM5266171 MCF7_Input_EV
GSM5266172 MCF7_Input_TET2_CD
GSM5266173 MCF7_Input_TET2_mCD
BioProject PRJNA725215
SRA SRP316406

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Supplementary file Size Download File type/resource
GSE173344_RAW.tar 4.4 Gb (http)(custom) TAR (of WIG)
GSE173344_matrix_gene_expression_RNAseq_rsem.txt.gz 2.0 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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