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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 06, 2018 |
| Title |
4B2N1-C3 |
| Sample type |
SRA |
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| Source name |
cell_WES
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| Organism |
Mus musculus |
| Characteristics |
cell type: haploid embryonic stem cells
strain: C57BL/6
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| 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).
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| 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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.
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| Submission date |
May 29, 2018 |
| Last update date |
Aug 06, 2018 |
| Contact name |
Qing Li |
| E-mail(s) |
[email protected]
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| Organization name |
Chinese Academy of Science
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| Department |
institute of biochemistry and cell biology
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| Lab |
Jinsong Li's Lab
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| Street address |
320 Yueyang Road
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE115017 |
Whole exome sequencing analyzed the off-target effect of gene editing through BE3 system. |
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| Relations |
| BioSample |
SAMN09274976 |
| SRA |
SRX4135976 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3163045_R18023917LU01-4B2N1-C3_SNP_INDEL_recal.vcf.gz |
501.2 Kb |
(ftp)(http) |
VCF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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