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Sample GSM2411238 Query DataSets for GSM2411238
Status Public on Dec 05, 2017
Title STEM-seq E6.5Epi_tetDKO_rep3
Sample type SRA
 
Source name embryo_Tet1/2 double knockout
Organism Mus musculus
Characteristics strain: C57BL/6N x DBA
genotype: Tet1/2 double knockout
developmental stage: E6.5
tissue: Epiblast
Treatment protocol Tet1+/- mice (B6;129S4-Tet1tm1.1Jae/J) and Tet2-/- mice (B6;129S-Tet2tm1.1Iaai/J ) were purchased from The Jackson Laboratory. After mating Tet1+/-/Tet2-/- heterozygotes, E6.5 epiblast from embryonic regions was collected from Tet1/2 DKO embryos as described above. Extraembryonic regions were used for genotyping.
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 2500
 
Description STEM-seq-methylC processed data file: GSE76505_E6.5Epi_tetDKO_merge_mCG.txt.
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 Nov 30, 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 GPL17021
Series (1)
GSE76505 Dynamic epigenomic landscapes during early lineage specification in mouse embryos
Relations
BioSample SAMN06090775
SRA SRX2385106

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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