|
| Status |
Public on Mar 28, 2012 |
| Title |
sperm X1-4 |
| Sample type |
SRA |
| |
|
| Source name |
sperm X1-4
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: sperm
strain: 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:
sperm-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 |
SRX119321 |
| BioSample |
SAMN00783979 |
