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Series GSE61133 Query DataSets for GSE61133
Status Public on Oct 30, 2015
Title MeDIP analysis of 5mC and 5hmC marks in human ataxia-telangiectasia cerebellum
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary Genomic DNA was prepared, fragmented, and immunoprecipitated with antibodies specific for 5mC or 5hmC prior to standard sequencing.

The neurodegenerative disease known as ataxia-telangiectasia (A-T) is caused by the absence of the ATM (A-T mutated) protein. A long-standing mystery surrounding A-T is why cerebellar Purkinje cells (PCs) appear uniquely vulnerable to ATM-deficiency. Here, we present that 5-hydroxymethylcytosine (5hmC), a newly recognized epigenetic marker found at high levels in neurons, is substantially reduced in human A-T and Atm-/- mouse cerebellar PCs. TET1, an enzyme that converts 5mC to 5hmC, responds to DNA damage. Manipulation of TET1 activity directly affects neuronal cell cycle reentry and cell death after the induction of DNA damage. Quantitative, genome-wide analysis of 5hmC of samples from human cerebellum showed that in ATM-deficiency there is a remarkable genome-wide reduction of 5hmC enrichment at both proximal and distal regulatory elements. These results reveal a role of TET1-mediated 5hmC in DNA damage response, and provide insights into the basis of a PC-specific DNA demethylation alteration in ATM-deficiency.
Overall design There are two groups, A-T and Control. For each group, cerebellar DNA samples were immunoprecipitated with anti-5mC (n=1) or anti-5hmC (n=3). There were also two replicates of input control for each group.
Contributor(s) Hart RP, Li J, Herrup K
Citation(s) 26510954
Submission date Sep 04, 2014
Last update date May 15, 2019
Contact name Ronald P. Hart
Phone 848-445-1783
Organization name Rutgers University
Department Cell Biology & Neuroscience
Street address 604 Allison Rd Rm B430
City Piscataway
State/province NJ
ZIP/Postal code 08854
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (12)
GSM1498150 23_AT_5hmc_input_rep1
GSM1498151 24_AT_5hmc_input_rep2
GSM1498152 15_AT_5hmc_IP_rep1
This SubSeries is part of SuperSeries:
GSE61169 Selective loss of 5hmC links to A-T Purkinje cell vulnerability
BioProject PRJNA260309
SRA SRP046261

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE61133_AT_5hmc_input_pooled.tagAlign.gz 430.9 Mb (ftp)(http) TAGALIGN
GSE61133_AT_5hmc_pooled.conservative.sort.bed.gz 427.1 Kb (ftp)(http) BED
GSE61133_AT_5hmc_pooled.tagAlign.gz 145.2 Mb (ftp)(http) TAGALIGN
GSE61133_Control_5hmc_input_pooled.tagAlign.gz 435.8 Mb (ftp)(http) TAGALIGN
GSE61133_Control_5hmc_pooled.conservative.sort.bed.gz 201.5 Kb (ftp)(http) BED
GSE61133_Control_5hmc_pooled.tagAlign.gz 200.2 Mb (ftp)(http) TAGALIGN
GSE61133_RAW.tar 1.3 Gb (http)(custom) TAR (of TAGALIGN)
GSE61133_readme.txt 1001 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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