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Series GSE77961 Query DataSets for GSE77961
Status Public on Feb 16, 2017
Title Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary We performed a parallel analysis of commonly used pre- and post-bisulfite WGBS library preparation protocols for their performance and quality of sequencing outputs. Our results show that bisulfite conversion per se generates pronounced sequencing biases, and subsequent fragmentation and amplification steps lead to several-fold overrepresentation of these artefacts. Standard pre-bisulfite library preparation methods lead to a significantly biased genomic sequence representation and a marked overestimation of methylation levels. We have integrated a bias diagnostic tool in the Bismark package and propose that amplification-free and post-bisulfite procedures should become the gold standard for WGBS library preparation.
Overall design WGBS (BS-seq) was performed on unmethylated or in vitro methylated triple-Dnmt-KO (TKO) mouse embryonic stem cells with two bisulfite conversion protocols - with either alkaline or heat denaturation. MeDIP input was used as a non-bisulfute converted genomic DNA control.
Contributor(s) Olova N, Krueger F, Andrews SR, Branco M, Reik W
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Submission date Feb 16, 2016
Last update date May 15, 2019
Contact name Gavin Kelsey
Organization name The Babraham Institute
Street address Babraham Research Campus
City Cambridge
ZIP/Postal code CB22 3AT
Country United Kingdom
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (16)
GSM2062450 Alkaline_2
GSM2062451 Alkaline_3
GSM2062452 Heat_1
BioProject PRJNA312207
SRA SRP070168

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE77961_MeDIP_Input_1kb_tiles_readcount.txt.gz 34.2 Mb (ftp)(http) TXT
GSE77961_RAW.tar 497.4 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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