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| Status |
Public on Sep 01, 2019 |
| Title |
WES_Kit_E251 |
| Sample type |
SRA |
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| Source name |
Mouse bone marrow cells
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| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: E2-KO
tissue: Bone marrow
cell type: c-Kit+ leukemia cells
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| Treatment protocol |
NA
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| Growth protocol |
Bone marrow cells were obtained by flushing femurs and tibias with a 25G needle or by crushing femurs, tibias, vertebrae and pelvic bones with a mortar in Ca2+ and Mg2+-free Hank’s buffered salt solution (HBSS; Gibco) supplemented with 2% heat-inactivated bovine serum (HIBS, Gibco). For flow cytometric analysis and isolation, cells were incubated with combinations of antibodies listed in the key resource table. Lineage markers for HSCs and progenitors were CD3, CD5, CD8, B220, Gr1 and Ter119. Antibody staining was performed at 4 °C for 30 min, or, when CD34 was included in the cocktail, on ice for 90 min. Biotinylated antibodies were visualized by incubation with PE/Cy7-conjugated streptavidin at 4°C for 30 min. DAPI (4′,6-diamidino-2-phenylindole; 2 μg/ml in PBS) or PI (propidium iodide; 1 μg/ml) were used to exclude dead cells during flow cytometry.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genome DNA were isolated from c-Kit+ leukemia cells from E2-KO moribund mice and processed for whole exome sequencing (WES) analysis using Agilent SureSelect XT Mouse All Exon Kit (cat# 1000001746) following manufacturer’s protocols.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Library strategy: WES
Raw reads were mapped to mouse genome mm10 (GRCm38) using SpeedSeq version 0.1.0 with default parameters.
The variants were detected using SpeedSeq version 0.1.0 and VarScan version 2.3.9.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: VCF format
Supplementary_files_format_and_content: Tab-delimited SNP and Indel calls.
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| Submission date |
Nov 15, 2018 |
| Last update date |
Sep 02, 2019 |
| Contact name |
Jian Xu |
| E-mail(s) |
[email protected]
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| Phone |
9015955208
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| Organization name |
St. Jude Children's Research Hospital
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| Department |
Pathology
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| Street address |
262 Danny Thomas Place, MS 345
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| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE122585 |
Whole exome sequencing analysis of bone marrow c-Kit+ leukemia cells in Nras-G12D with Ezh2 KO (E2-KO) mice |
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| Relations |
| BioSample |
SAMN10431973 |
| SRA |
SRX5012077 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3475297_WES_Kit_E251_SpeedSeq.vcf.txt.gz |
6.9 Mb |
(ftp)(http) |
TXT |
| GSM3475297_WES_Kit_E251_VarScan2.indel.txt.gz |
190.2 Kb |
(ftp)(http) |
TXT |
| GSM3475297_WES_Kit_E251_VarScan2.snp.txt.gz |
978.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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