|
| Status |
Public on Sep 30, 2017 |
| Title |
Zygote_CZ_1 |
| Sample type |
SRA |
| |
|
| Source name |
zygote from Cxxc1fl/fl;Zp3-Cre female and wildtype male
|
| Organism |
Mus musculus |
| Characteristics |
cell type: zygote
|
| Extracted molecule |
total RNA |
| Extraction protocol |
for transcriptome analysis, oocytes or embryos were extracted from mouse ovary or fallopian tube and put in 350ul RLT buffer（QIAGEN）acutely vortexed for 1min, and RNA was harvested using RNeasy micro kit.NEBNext® Ultra™ RNA Library Prep Kit for Illumina were used for the construction of sequencing libraries.for methylation analysis,200 GV oocytes were extracted from 3week female mouse and put in lysis buffer to release the genomic DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols;then whole genome bisulfite sequencing library was prepared using method published by S.A. smallwood et.al(2014)
RNA-Seq; single cell whole genome bisulfite sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the mm10 genome assembly using Tophat(version 2.0.12)
the expression level were calculated and normalized by cufflinks(version 2.2.1)
Bisulfite sequencing reads were mapping to the converted mm9 genome using bismark(version 0.7.6)
5mC were called with samtools.
Genome_build: mm9 and mm10
|
| |
|
| Submission date |
Jul 31, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaoying Fan |
| E-mail(s) |
sharryfan100@gmail.com
|
| Organization name |
Peking University
|
| Department |
College of Life Sciences
|
| Lab |
Biodynamic Optical Imaging Center
|
| Street address |
5 Yiheyuan Road
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE85019 |
CFP1 Regulates Histone H3K4 Trimethylation and Developmental Potential in Mouse Oocytes |
|
| Relations |
| BioSample |
SAMN05467109 |
| SRA |
SRX1992133 |
