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Series GSE77967 Query DataSets for GSE77967
Status Public on Sep 01, 2016
Title A highly sensitive and robust method for genome-wide 5hmC profiling of rare cell populations
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Investigations of 5-hydroxymethylcytosine (5hmC) in biologically and clinically samples and models with low cell numbers have been hampered by the low sensitivity and reproducibility using current 5hmC mapping approaches. Here, we develop a selective 5hmC chemical labeling approach using tagmentation-based library preparation in order to profile nanogram levels of 5hmC isolated from ~1,000 cells (nano-hmC-Seal). Using this technology, we profiled the dynamics of 5hmC across different stages of mouse hematopoietic differentiation. Additionally, applying nano-hmC-Seal to the hematopoietic multipotent progenitor cells in an acute myeloid leukemia (AML) mouse model, we identified leukemia-specific, differentially hydroxymethylated regions that harbor previously reported and as-yet-unidentified functionally relevant factors. The change of 5hmC patterns in AML strongly correlates with the altered gene expression on a global scale. Together, our new approach offers a highly sensitive and robust method to study and detect DNA methylation dynamics from in vivo model and clinical samples.
 
Overall design Selective 5hmC chemical labeling approach using tagmentation-based library preparation in order to profile nanogram levels of 5hmC isolated from ~1,000 cells
 
Contributor(s) Han D, Lu X, Shih AH, Levine RL, He C
Citation(s) 27477909
Submission date Feb 16, 2016
Last update date May 15, 2019
Contact name Dali Han
E-mail(s) handali294@gmail.com
Organization name University of Chicago
Department Department of Chemisty
Street address 5801 South Ellis Avenue
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (56)
GSM2062718 hematopoiesis_lsk_1
GSM2062719 hematopoiesis_lsk_2
GSM2062720 hematopoiesis_lsk_3
Relations
BioProject PRJNA312218
SRA SRP070188

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
GSE77967_RAW.tar 2.6 Gb (http)(custom) TAR (of BEDGRAPH)
GSE77967_RNASeq_rld_expr.txt.gz 1.6 Mb (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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