|
| Status |
Public on Oct 21, 2016 |
| Title |
CLL_Normal_SS198_Normal |
| Sample type |
genomic |
| |
|
| Source name |
Saliva CLL_Normal_SS198_Normal
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: saliva
tissue source: CLL -Matched Normal
|
| Treatment protocol |
B cell enrichment was performed using Easy Sep Human B cell Enrichment Kit (StemCell Technologies Inc, Vancouver, Canada) for samples with WBC count lower than 25K or absolute lymphocyte count <20K. For samples with lymphocyte count >25K, peripheral blood mononuclear cells (PBMC) were separated using conventional Ficoll-Hypaque separation according to manufacturer’s instructions (StemCell Techonologies Inc, Vancouver, Canada).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumor and saliva DNA were extracted using QIAamp Blood DNA (Qiagen Inc, Valencia, CA) and Oragene DNA (Oragene, Ontario, Canada) kits respectively, according to the manufacturer’s directions.
|
| Label |
Biotin
|
| Label protocol |
Samples for Affymetrix CytoScan HD arrays were labelled following fragmentation according to the manufacturer’s protocol.
|
| |
|
| Hybridization protocol |
Standard protocols detailed by the manufacturer (Affymetrix Inc.) was used for array hybridization. The arrays were hybridized using the Hybridization Oven 645.
|
| Scan protocol |
The arrays were scanned according to the standard protocol using the Gene Chip Scanner 3000 (Affymetrix Inc)
|
| Description |
processed data file: SS198Final.txt
|
| Data processing |
Raw data was processed using the Affymetrix Chromosome Analysis Suite [version -2.0.1.2 (r5919)], genome build hg19. Reference model file used was "CytoScanHD_Array.na32.3.v1.REF_MODEL" and the annotation file used was "CytoScanHD_Arra_na32.3.annot.db".
A cutoff of 25 probes and 200kb (50 kb on gene overlapping regions) for deletion CNAs or 400kb (50 kb on gene overlapping regions) for gain CNAs was used. A size cut off of 10 MB genome-wide and 3 MB within genic regions was used to detect LOH events. All CNAs and LOHs were manually reviewed. The TXT format file of the final data can be found in a tar archive on the series record.
|
| |
|
| Submission date |
Oct 21, 2015 |
| Last update date |
Oct 21, 2016 |
| Contact name |
Sunita R Setlur |
| E-mail(s) |
[email protected]
|
| Organization name |
Brigham and Women's Hospital
|
| Street address |
221 Longwood Avenue
|
| City |
Boston |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL16131 |
| Series (1) |
| GSE74239 |
Affymetrix CytoScan HD array data for del(17p) Chronic Lymphocytic Leukemia samples |
|
