|
| Status |
Public on Nov 08, 2021 |
| Title |
wild type C57BL/6 #1 |
| Sample type |
SRA |
| |
|
| Source name |
wild type C57BL/6 #1
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
genotype: sex age matched wild type
timepoint: baseline
cell type: purified bone marrow
|
| Growth protocol |
tertiary MLL-AF9 leukemic cells were harvested from the bone marrow of secondary recipient C57BL/6 mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Viable leukemic cells were sorted on the BD FACSAria III. Genomic DNA was purified with the Qiagen Dneasy blood and tissue kit.
300 ng of DNA was fragmented to approximately 200 bp using a focal acoustic device (Covaris S2, Sage Sciences). Libraries were prepared with NEB-Next Ultra II Kit (NEB) according to the manufacturer’s instructions
low coverage wgs
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
low coverage wgs of purified bone marrow
|
| Data processing |
raw sequencing reads were cleaned with cutadapt (v1.9.1) and aligned with BWA (v0.7.13) to reference genome GRCm38.78. PCR duplicates were marked with picard (v2.17.3) and removed using Samtools (v1.9). Copy number analysis was performed using QDNASeq (version 1.26.0). The genome was divided into nonoverlapping 15-kb bins, and the number of reads mapping within each bin was counted and adjusted with a simultaneous 2D locally estimated scatterplot smoothing (LOESS) correction accounting for read mappability and GC content. All other QDNASeq parameters were set as default. Copy number changes were reported as transformed absolute copy number values (log2(absolute copy number) −1).
Genome_build: mm10
Supplementary_files_format_and_content: log2 normalized genome segment files
|
| |
|
| Submission date |
Oct 21, 2021 |
| 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) |
| GSE161676 |
Identifying non-genetic determinants of malignant clonal fitness at single cell resolution |
| GSE186307 |
Identifying non-genetic determinants of malignant clonal fitness at single cell resolution [tertiary leukemia LC-WGS] |
|
| Relations |
| BioSample |
SAMN22458226 |
| SRA |
SRX12722933 |
