|
| Status |
Public on Nov 08, 2021 |
| Title |
MLL-AF9 + Flt3 ITD/ITD rep1 |
| Sample type |
SRA |
| |
|
| Source name |
cKit + progenitors
|
| Organism |
Mus musculus |
| Characteristics |
tissue: haematopoietic progenitors
mutation: MLL-AF9 + Flt3 ITD/ITD
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from mouse whole bone marrow cells using the Qiagen DNeasy Blood and Tissue Kit
Exonic DNA fragments were captured from genomic DNA using the Agilent SureSelectXT Mouse All Exon kit.
Exome-Seq
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned with BWA (v0.7.13) to reference genome GRCm38.78 and duplicates marked with picard (v2.17.3).
Variant calling was performed with Strelka2 somatic workflow (v2.9.10), which includes structural variant calling with Manta (v1.5). PASS variants from variant calling were annotated with VEP (v92).
Compiled variants were filtered by variant allele frequency with respect to the initiating variant of their respective groups (~30%) to filter out sub-clonal mutations.
Genome_build: mm10
|
| |
|
| Submission date |
Nov 17, 2020 |
| Last update date |
Nov 08, 2021 |
| Contact name |
Mark Dawson |
| E-mail(s) |
mark.dawson@petermac.org
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
305 Grattan Street
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE161661 |
Identifying non-genetic determinants of malignant clonal fitness at single cell resolution (secondary leukaemia exome) |
| GSE161676 |
Identifying non-genetic determinants of malignant clonal fitness at single cell resolution |
|
| Relations |
| BioSample |
SAMN16822509 |
| SRA |
SRX9522810 |
