|
| Status |
Public on Jul 30, 2014 |
| Title |
CD19-enriched CLL patient sample, patient #3107 |
| Sample type |
RNA |
| |
|
| Source name |
CLL clinical sample, CD19-enriched
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: relapsed chronic lymphocytic leukemia (CLL) patient
patient id: patient #3107
binet stage: C
tissue: CD19-enriched CLL patient sample
|
| Treatment protocol |
not applicable
|
| Growth protocol |
Pretreatment specimens from relapsed chronic lymphocytic leukemia patients
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CLL samples were positively enriched by magnetic cell sorting using CD19 microbeads and MACS columns (Miltenyi Biotec Ltd, Surrey, UK). Total RNA was isolated using Trizol (Invitrogen) and RNeasy kit (QIAGEN).
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials per manufacturers recommendation. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 (fluidics protocol FS450_0001).
|
| Scan protocol |
Arrays were scanned using the Affymetrix GCS 3000 7G and Gene-Chip Operating Software v.1.3.0 to produce .CEL intensity files.
|
| Description |
CD19-enriched CLL clinical sample
A0020404
|
| Data processing |
.CEL files were background adjusted, quantile normalized and summarized at the transcript level using only core probesets that mapped to RefSeq transcripts, by apt (Affymetrix Power Tool version 1.12.0) software that used the RMA algorithm.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.na29.hg18.probeset.csv
|
| |
|
| Submission date |
Jun 05, 2014 |
| Last update date |
Jul 30, 2014 |
| Contact name |
Ru-Fang Yeh |
| E-mail(s) |
yeh.rufang@gene.com
|
| Organization name |
Genentech
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94040 |
| Country |
USA |
| |
|
| Platform ID |
GPL18761 |
| Series (1) |
| GSE58211 |
Expression data of chronic lymphocytic leukemia patient samples from the REACH study |
|
