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Sample GSM3163050 Query DataSets for GSM3163050
Status Public on Aug 06, 2018
Title 4B2N1-E5
Sample type SRA
Source name embryo_WES
Organism Mus musculus
Characteristics developmental stage: E12.5 embryo
generation: F1
strain: C57BL/6 X DBA2
tissue: tail
Growth protocol Haploid stem cells were maintained in DMEM (Millipore) with 15% FBS (Gibco), Penicillin-Streptomycin, NEAA, NUC, L-glutamine, β-mercaptoethanol, 1000 U/ml Lif, 1 μM PD03259010 (Selleck) and 3 μM CHIR99021 (Selleck).
Extracted molecule genomic DNA
Extraction protocol Mouse genomic DNA of cells and mice was isolated using the TIANamp Genomic DNA Kit (TIANGEN)
Firstly, the genomic DNA randomly break into 150~300 bp by ultrasonic apparatus and purified with magnetic beads. Then, the product requires end repair, A-tailing, adapter ligation. The ligated products need to purify with magnetic beads again and obtain library through PCR amplification. The library was captured by Agilent Sure Select Mouse All Exon Kit and purified, amplified. The quality of sequencing library tested by Qubit and Agilent 2100 Bioanalyzer.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
Data processing Library strategy: WES
QC control: FastQC version: 0.11.2
Trim: trimmomatic version: 0.36, parameters: PE AVGQUAL:20 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50
Alignment: All reads were aligned to the mm10 genome assembly using BWA-MEM with default parameters
SNP/InDel analysis: SNV and InDel were called and annotated according to Sentieon(201611.02) pipelines
Genome_build: mm10
Supplementary_files_format_and_content: Vcf formate contianed SNP and indel summary for each samples.
Submission date May 29, 2018
Last update date Aug 06, 2018
Contact name Qing Li
Organization name Chinese Academy of Science
Department institute of biochemistry and cell biology
Lab Jinsong Li's Lab
Street address 320 Yueyang Road
City Shanghai
ZIP/Postal code 200031
Country China
Platform ID GPL24247
Series (1)
GSE115017 Whole exome sequencing analyzed the off-target effect of gene editing through BE3 system.
BioSample SAMN09274971
SRA SRX4135981

Supplementary file Size Download File type/resource
GSM3163050_R18020032LU01-4B2N1-E5_SNP_INDEL_recal.vcf.gz 3.7 Mb (ftp)(http) VCF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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