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Sample GSM2027226 Query DataSets for GSM2027226
Status Public on Dec 05, 2017
Title STEM-seq E3.5ICM
Sample type SRA
 
Source name Preimplantation embryo_E3.5 Inner cell mass
Organism Mus musculus
Characteristics strain: C57BL/6N x DBA/2N
developmental stage: E3.5
tissue: Inner cell mass
Treatment protocol C57BL/6N female mice were induced for superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin and 5 IU of human chorionic gonadotrophin (44-48 hours apart) and mated to DBA/2N males.
Extracted molecule genomic DNA
Extraction protocol Embryos were washed with PBS and incubated in lysis buffer. STEM-seq libraries were constructed following the protocol described in this study (Zhang et al., Nature Genetics, 2017).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 1500
 
Description Processed data file: stage.mCG.gz in STEM-seq-methylC_mCG.tar.gz.
The format for mCG files is as below:
chr position methylated_crick, un-methylated_crick, methylated_watson, un-methylated watson.
Data processing Base calls were performed using CASAVA version 1.8. Early embryo STEM-seq reads were aligned to the mm9 genome using BSseeker2.0.8. Replicates of same stage were pooled together and methylation values in wiggle files were computed for each single base. ES cell STEM-seq and MethylC-seq reads were aligned to the mm9 genome using BSseeker2.0.8. Replicates of same stage were pooled together and methylation values in wiggle files were computed by the number of reads falling into 1,000bp bin in the genome.
Genome_build: mm9.
Supplementary_files_format_and_content: The bedgraph files counted the number of reads falling on each base or 1,000bp bin in the genome.
 
Submission date Jan 04, 2016
Last update date May 15, 2019
Contact name Wei Xie
E-mail(s) xiewei121@tsinghua.edu.cn
Organization name Tsinghua University
Street address Zhongguancun north street
City Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL18480
Series (1)
GSE76505 Dynamic epigenomic landscapes during early lineage specification in mouse embryos
Relations
BioSample SAMN04383643
SRA SRX1515392

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

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