NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5643591 Query DataSets for GSM5643591
Status Public on Nov 08, 2021
Title tertiary MLL-AF9 #2
Sample type SRA
 
Source name tertiary MLL-AF9 #2
Organism Mus musculus
Characteristics tissue: bone marrow
genotype: M3
timepoint: baseline
cell type: purified leukemic cells from 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 leukemic cells from 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 SAMN22458229
SRA SRX12722936

Supplementary file Size Download File type/resource
GSM5643591_WGS_KF09_M3_H3GYWDSX2_TCCTCATG_L002_filtered.rmdup.seg.gz 404 b (ftp)(http) SEG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap