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Sample GSM2256372 Query DataSets for GSM2256372
Status Public on Sep 30, 2017
Title Zygote_CZ_3
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 SAMN05467107
SRA SRX1992135

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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