|
| Status |
Public on Sep 02, 2021 |
| Title |
TS042811A_snp |
| Sample type |
genomic |
| |
|
| Source name |
CD19+ B cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: tonsil
disease state: healthy
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from sorted B CD19+ B cells using a Qiagen Dneasy Blood and Tissue kit.
|
| Label |
Biotin
|
| Label protocol |
Per manufacturer's instructions
|
| |
|
| Hybridization protocol |
0.5 ug of DNA was hybridized according to manufacturer's instructions.
|
| Scan protocol |
GS3000
|
| Data processing |
Genotypes were called from CEL files using the Affymetrix Genotyping Console (v4.2.0.26) with the BIRDSEED v2 algorithm with default settings. Copy number analysis was performed with the Affymetrix Genotyping Console using regional GC correction and default settings. The DNAcopy R package was used for circular binary segmentation on raw data. cnvkit and the copynumber R package were used for CNV thresholding using log2 ratio values of -0.2 and 0.2.
|
| |
|
| Submission date |
Feb 24, 2020 |
| Last update date |
Sep 02, 2021 |
| Contact name |
Jared Andrews |
| E-mail(s) |
jared.andrews@stjude.org
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Developmental Neurobiology
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE145846 |
Key Super Enhancers Drive Tumor-Suppressing Transcription Feedback Programs in Mature B Cell Cancers (SNP array) |
| GSE145848 |
Key Super Enhancers Drive Tumor-Suppressing Transcription Feedback Programs in Mature B Cell Cancers |
|
