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Sample GSM870000 Query DataSets for GSM870000
Status Public on Mar 28, 2012
Title zygote NoPB2-BDF1-X1-4
Sample type SRA
 
Source name zygote No PB
Organism Mus musculus
Characteristics developmental stage: zygote
treatment: polar body removed
strain: BDF1-X1
Treatment protocol NoPB embryos were subjected to laser assisted polar body biopsy using an 8 mm piezo pipette in batches of 5 embryos in M2 medium microdrops (Millipore) under mineral oil and cultured to the described stage. ICM was isolated using rabbit anti mouse serum (Sigma Aldrich) and Guinea pig complement serum to ablate the outer trophectoderm of E3.5 blastocysts. E6.5 and E7.5 embryos were dissected from the implanted decidua in PBS.
Growth protocol Isolated embryos were cultured in C02 buffered KSOM medium supplemented with amino acids (Millipore) until isolation at a perscribed stage. Oocytes and embryos were isolated from gonadotropin primed females and sperm collected from the cauda epidinymis of recently mated male mice
Extracted molecule genomic DNA
Extraction protocol Reduced representation bisulfite libraries were prepared from Proteinase K treated, MspI digested DNA following ligation with methylated standard adapters, size selection, bisulfite conversion, and amplification of the final libraries
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina Genome Analyzer IIx
 
Description Msp1 digested bisulfite converted genomic DNA
Reduced representation bisulfite sequencing libraries are designed to enrich for a consistent subset of CpGs in the genome using MspI digestion (C'CGG cutting), adapater ligation and bisulfite conversion to generate base resolution maps of cytosine methylation on a consistent genome scale
Data processing Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.
Genome Build:
zygoteNoPB2-BDF1-X1-4.cpgs.txt: mm9
 
Submission date Feb 02, 2012
Last update date May 15, 2019
Contact name Michelle M Chan
Organization name UCSF
Lab Weissman Lab
Street address 1700 4th St.
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platform ID GPL11002
Series (1)
GSE34864 A unique regulatory phase of DNA methylation in the early mammalian embryo
Relations
Reanalyzed by GSE38711
SRA SRX119312
BioSample SAMN00783970

Supplementary file Size Download File type/resource
GSM870000_zygoteNoPB2-BDF1-X1-4.cpgs.txt.gz 7.1 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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