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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 01, 2023 |
| Title |
SNV, INDEL, CNV of WGS, AML |
| Sample type |
SRA |
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| Source name |
Mac1+Gr1+GFP+
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Bone marrow
cell stage: 8-10 weeks
cell type: Mac1+Gr1+GFP+
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole genome sequencing (WGS) analysis was performed on B-ALL, T-ALL, AML and AUL samples to detect mutations and integration sites of retroviral N-Myc. 2x106 GFP+ leukemia cells collected from B-ALL, T-ALL, AML, and AUL mice, and stocked at -80℃. Genomic DNAs were extracted from samples. DNA concentration ≥20 ng/µL, and DNA mass≥0.2 µg were used for the quality control (Qubit 2.0 software).
350 bp of DNA fragments were produced by Covaris ultrasonicator, followed by end-repair, phosphorylation, and adding A-tailing to DNA fragments. P5 adaptor (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and P7 adaptor (5’-GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG-3’) were used for library construction. The quality of DNA library was tested by Agilent 2100 and Q-PCR. The DNA library was sequenced under 30x sequencing depth by Illumina HiSeq PE150 (Pair End 150 bp) at Novogene.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Library strategy: WGS
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using BWA (Li H et al.) and Samblaster
The alignment of BAM file was performed by Samblaster
The multiple hits for SNP, INDEL, CNV and integration site of N-Myc
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files for each Sample
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| Submission date |
Mar 04, 2020 |
| Last update date |
Mar 01, 2023 |
| Contact name |
Haitao Bai |
| E-mail(s) |
zhangqingyun@ihcams.ac.cn
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| Organization name |
Chinese Academy of Medical Sciences
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| Department |
Institute of Hematology & Blood Diseases Hospital
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| Street address |
288 Nanjing Road
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| City |
Tianjin |
| State/province |
Tianjin |
| ZIP/Postal code |
300020 |
| Country |
China |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE146331 |
N-Myc overexpression leads to multiple types of acute leukemia in mice [WGS] |
| GSE146333 |
N-Myc overexpression leads to multiple types of acute leukemia in mice |
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| Relations |
| BioSample |
SAMN14278846 |
| SRA |
SRX7846732 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4378204_AML.freec.cnv.mm10_multianno.txt.gz |
32.8 Kb |
(ftp)(http) |
TXT |
| GSM4378204_AML.samtools.indel.annovar.mm10_multianno.txt.gz |
9.6 Mb |
(ftp)(http) |
TXT |
| GSM4378204_AML.samtools.snp.annovar.mm10_multianno.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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