|
| Status |
Public on May 31, 2023 |
| Title |
DLBCL [Sample_032] |
| Sample type |
genomic |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Diffuse large B-cell lymphoma (DLBCL)
Stage: 2
treatment: Yes
progression: No
dead: No
gender: Female
age: Adult
tissue: Blood
|
| Treatment protocol |
All patients were treated with the R-CHOP 21 protocol.
|
| Growth protocol |
Not applicable.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Puregene Blood Core Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
DNA was restriction digested, PCR amplified, fragmented, and labeled according to the manufacturer (Affymetrix).
|
| |
|
| Hybridization protocol |
DNA was hybridized to each array according to the manufacturer's instructions. The arrays were then washed using Affymetrix Fluidics Stations.
|
| Scan protocol |
The arrays were scanned using the Gene Chip Scanner 3000.
|
| Description |
Sample_032.CEL
|
| Data processing |
Files of .CEL type were imported in the Axiom Analysis Suite (Thermo Fisher Scientific. Axiom Genotyping Solution - Data Analysis Guide. Tech. Rep. 2011) and processed using the Axiom UKB WCSG array type to evaluate sample and SNP quality. In case of more than one probeset interrogating the same SNP, the best probeset was chosen according to the “BestProbeSet” variable and then, according to Axiom Analysis Suite metrics, SNPs quality was checked. In particular, monomorphic SNPs and SNPs with a call rate <95% were filtered. Fisher’s Linear Discriminant (FLD), Homozygous Ratio Offset (HomRO) and Heterozygous Strength Offset (HetSO) thresholds were also considered. Default cut-offs were used.
AxiomGT1_intensity.txt: Tab-delmited text file includes signal intensity of both alleles.
AxiomGT1_genotype_calls3.txt: Tab-delmited text file includes Genotype Calls (SNP calls): AA, AB, BB, No Call.
|
| |
|
| Submission date |
Oct 22, 2021 |
| Last update date |
May 31, 2023 |
| Contact name |
Stefania Nobili |
| E-mail(s) |
stefania.nobili@unifi.it
|
| Organization name |
University of Florence
|
| Department |
Health Sciences
|
| Street address |
viale Pieraccini 6
|
| City |
Firenze |
| ZIP/Postal code |
50139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL28377 |
| Series (1) |
| GSE186441 |
Genome-wide single nucleotide polymorphism analysis identifies DNA variations predictive of R-CHOP efficacy in diffuse large B-cell lymphoma |
|
