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Series GSE74850 Query DataSets for GSE74850
Status Public on Jan 04, 2016
Title Effects of dynamic cytosine methylation on alternative pre-mRNA splicing in T lymphocytes
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Intragenic 5-methylcytosine and CTCF mediate opposing affects on pre-mRNA splicing: CTCF promotes inclusion of weak upstream exons through RNA polymerase II pausing, whereas 5-methylcytosine evicts CTCF, leading to exon exclusion. However, the mechanisms governing dynamic DNA methylation at CTCF binding sites were unclear. In this study, we identify the methylcytosine dioxygenases TET1 and TET2 as active regulators of CTCF-mediated alternative splicing through conversion of 5-methylcytosine to its oxidation derivatives.
 
Overall design Transcriptional profiling of human T-lymphocytes in the naïve and activated states was performed by RNA-Seq. Methylation status (5mC and 5hmC) was assayed by medIP-Seq. CTCF binding sites were identified by ChIP-Seq.
 
Contributor(s) Marina R, Sturgill D, Thenoz M, Bailly M, Singh G, Prigge M, Nanan K, Shukla S, Haque N, Oberdoerffer S
Citation(s) 26711177
Submission date Nov 10, 2015
Last update date May 15, 2019
Contact name David Sturgill
E-mail(s) davidsturgill@mail.nih.gov
Phone 240-760-6725
Organization name NIH
Department NCI
Lab LRBGE
Street address Building 41, Rm B622
City Bethesda
State/province MARYLAND
ZIP/Postal code 20892
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (14)
GSM1936633 Naive_Tcell_RNA-Seq
GSM1936634 Activated_Tcell_RNA-Seq
GSM1936635 Naive_CTCF_ChIP-Seq_10_12
Relations
BioProject PRJNA301681
SRA SRP065988

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
GSE74850_RAW.tar 1.4 Gb (http)(custom) TAR (of BED, BW, FPKM_TRACKING)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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