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Series GSE41912 Query DataSets for GSE41912
Status Public on Nov 20, 2012
Title Transcriptome profiling of wild type and Tet1-null primordial germ cells (PGC) by Bisulfite-seq
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Purpose: To investigate the effect of Tet1 depletion on global DNA methylation, we performed whole-genome bisulfite sequencing (WGBS).
Methods: Starting with as little as 1400-5251 manually micro-dissected PGCs, we used an ultra-low input method, Tn5mC-seq.
Results: We generated 945 million reads for Tet1Gt/Gt PGCs and 302 million reads for wild-type PGCs. We obtained 14-16 million CpG sites per genotype at 1.76-2.66x genome coverage, which enables a comprehensive view of genome-wide DNA methylation patterns in E13.5 PGCs. PGCs are almost completely unmethylated genome-wide. Loss of Tet1 led to a subtle increase of methylation level in various genomic elements including promoters, exons, introns and repetitive elements in Tet1Gt/Gt PGCs (p<0.01). Local analysis identified 4,337 differentially methylated regions (DMRs) between Tet1-/- PGCs and wild-type cells. These DMRs are associated with 5,261 genes, among which 271 genes also exhibited differential gene expression and enriched for the cell cycle pathway (FDR=0.02).
Conclusions: This result revealed that demethylation of certain set of cell cycle genes is largely abolished in the Tet1-/- PGCs.
Overall design Genome-wide methylation profiles of primordial germ cells derived from the wild type (WT) and Tet1-null female embryos at E13.5 were generated by whole genome bisulfite sequencing using Illumina Hiseq.
Citation(s) 23151479
Submission date Oct 29, 2012
Last update date May 15, 2019
Contact name Kun Zhang
Organization name University of California, San Diego
Department Bioengineering
Lab Integrative Genomics Laboratory
Street address 9500 Gilman Dr Mailcode: 0412
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (9)
GSM1037870 Tet1-/- rep1
GSM1037871 Tet1-/- rep2
GSM1037872 Tet1-/- rep3
SRA SRP016883
BioProject PRJNA181955

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Supplementary file Size Download File type/resource
GSE41912_PGC-KO-all-chrs.BED.gz 138.7 Mb (ftp)(http) BED
GSE41912_PGC-WT-all-chrs.BED.gz 114.2 Mb (ftp)(http) BED
GSE41912_filter_unconverted_reads.txt.gz 717 b (ftp)(http) TXT
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