|
| Status |
Public on May 29, 2024 |
| Title |
WES Empty 1 |
| Sample type |
SRA |
| |
|
| Source name |
BM
|
| Organism |
Mus musculus |
| Characteristics |
tissue: BM
cell line: primary cell
cell type: Hematopoietic stem and progenitor cells
genotype: miR-146a wildtype/Runx1 wildtype
|
| Growth protocol |
genomic DNA isolated from FACS sorted BM GFP+/lin-/ckit+/Sca+ cells from WT/vector (n=3), WT/RUNX1mut (n=3), miR-146aKO/vector (n = 3), and miR-146aKO/RUNX1mut secondary transplanted mice were submitted to Otogenetics Corporation (Atlanta, GA, USA) for mouse exome capture and sequencing
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted using the AllPrep micro kit from Qiagen following manufacturer recommendations
SureSelect_Mouse_All_Exon_V1_Annotated_mm10_liftover_09212015.bed
Mouse exome sequencing from gDNA; Initial sample QC; Illumina library prep/QC; Agilent SureSelect mouse(51Mb), capture/QC; HiSeq2000/2500 PE100-125, designate average coverage of 30x
Exome sequencing
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Empty 1
|
| Data processing |
The quality of reads were checked using FastQC (v0.11.2).
Paired-end reads were aligned against the GRCm38 genome using BWA (v0.7.17).
Germline SNP and INDEL variants were separately detected using VarScan (v2.3.9) and Samtools (v1.8.0).
The exon target capture info was from Agilent SureSelect XT Mouse All Exon V1
Variants were annotated using VEP (v96).
Assembly: GRCm38
Supplementary files format and content: Predicted SNP and INDEL reports in the VCF format
|
| |
|
| Submission date |
Apr 15, 2024 |
| Last update date |
May 29, 2024 |
| Contact name |
Kwangmin Choi |
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Experimental Hematology & Cancer Biology
|
| Street address |
333 Burnet Avenue
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE264052 |
Dysregulated innate immune signaling cooperates with RUNX1 mutations to transform an MDS-like disease to AML (WES) |
| GSE264053 |
Dysregulated innate immune signaling cooperates with RUNX1 mutations to transform an MDS-like disease to AML |
|
| Relations |
| BioSample |
SAMN40975111 |
| SRA |
SRX24268216 |
