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Sample GSM5722894 Query DataSets for GSM5722894
Status Public on Dec 10, 2021
Title Bone marrow cells - SNP array (1149317-5)
Sample type genomic
 
Source name Bone marrow cells
Organism Homo sapiens
Characteristics disease state: Ph-positive ALL
treatment: HCVAD_plus_ponatinib
tissue: bone marrow
cell type: leukemic cell
Sex: Female
age_diagnosis: 53
outcome: Complete Response
Treatment protocol Samples were either bone marrow aspirate or peripheral blood obtained from previously untreated patients.
Growth protocol Not applicable
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from bone marrow or peripheral blood samples using a QIAamp DNA Mini kit (QIAGEN, Hilden, Germany).
Label Cy3 and Cy5
Label protocol standard Illumina protocol
 
Hybridization protocol According to the hybridazation protocol in manufacture's Reference Guide
Scan protocol According to the scan protocol in manufacture's Reference Guide
Data processing The raw data retrieved from an Illumina Omni2.5-8 SNP array was processed using GenomeStudio 2.0.
The raw log R ratio was used for ASCAT (allele-specific copy number analysis of tumors) algorithm to identify allele-specific copy-number alterations.
The log R ratio (LRR)
 
Submission date Dec 07, 2021
Last update date Dec 10, 2021
Contact name Yuya Sasaki
E-mail(s) imagingbio0311@gmail.com
Organization name M.D. Anderson Cancer Center
Street address 1515 Holcombe Blvd
City Houston
State/province TX
ZIP/Postal code 77054
Country USA
 
Platform ID GPL18952
Series (2)
GSE190392 Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios [Omni2.5]
GSE190397 Philadelphia chromosome (Ph)-positive acute lymphoblastic leukemia (ALL)

Supplementary data files not provided
Processed data are available on Series record

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