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Series GSE80973 Query DataSets for GSE80973
Status Public on May 03, 2016
Title Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction
Organisms Mus musculus; synthetic construct
Experiment type Methylation profiling by high throughput sequencing
Summary The epigenetic DNA modification 5-hydroxymethylcytosine (5hmC) has crucial roles in development and gene regulation. Quantifying the abundance of this epigenetic mark at the single-cell level could enable us to understand its roles. We present a single-cell, genome-wide and strand-specific 5hmC sequencing technology based on 5hmC glucosylation and glucosylation-dependent digestion of DNA, that reveals pronounced cell-to-cell variability in the abundance of 5hmC on the two DNA strands of a given chromosome. We develop a mathematical model that reproduces the strand bias and use this model to make two main predictions. First, the variation in strand bias should decrease when 5hmC turnover increases. Second, the strand bias of two sister cells should be strongly anti-correlated. We validate these predictions experimentally, and use our model to reconstruct lineages of 2- and 4-cell mouse embryos, showing that single-cell 5hmC sequencing can be used as a lineage reconstruction tool.
Overall design In this study, 5-hydroxymethylcytosine (5hmC) was detected on a genome-wide level in single cells from E14tg2a (E14) mouse embryonic stem cells, Vitamin C treated E14 cells, B6/CBA mouse oocytes, 2-cell mouse embryos and 4-cell mouse embryos using a new method called as scAba-seq.
Contributor(s) Mooijman D, Dey SS, Boisset J, Crosetto N, van Oudenaarden A
Citation(s) 27347753
Submission date May 02, 2016
Last update date May 15, 2019
Contact name Siddharth Subhas Dey
Organization name Hubrecht Institute
Lab van Oudenaarden lab
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL19424 Illumina NextSeq 500 (synthetic construct)
Samples (10)
GSM2139461 E14 single cells - Library 1
GSM2139462 E14 single cells - Library 2
GSM2139463 E14 single cells - Library 3
BioProject PRJNA320216
SRA SRP074232

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Supplementary file Size Download File type/resource
GSE80973_RAW.tar 123.3 Mb (http)(custom) TAR (of TXT)
GSE80973_README.txt.gz 1.4 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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