|
| Status |
Public on Jun 30, 2021 |
| Title |
CLLCCAID2386 |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: chronic lymphocytic leukaemia
prognostic association with gep signature: aggressive GEP signature
antibody pretreatment: Rituximab-naive
sensitivity to chemotherapy: Fludarabine untreated/sensitive
ecog: ECOG≤1
clinical course: early progression
|
| Treatment protocol |
Ficoll density gradient centrifugation for isolation of mononuclear cells with or without subsequent immunomagnetic tumor cell enrichment via CD19.
|
| Growth protocol |
Peripheral blood mononuclear cells were collected from CLL patients before initiation of treatment on randomized trial with fludarabine and cyclophosphomide +/- rituximab.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA for mRNA profiling was extracted from whole cell lysates of CLL patient samples according to the Allprep DNA/RNA mini kit (Qiagen). Quality control was assessed using the Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip (Agilent Technologies). RNA for gene expression profiling had a RIN of at least 7.
|
| Label |
Biotin
|
| Label protocol |
Samples from CLL patients were analyzed for mRNA expression using the Affymetrix GeneChip® Human Exon 1.0 ST Array (Affymetrix, Santa Clara, CA, USA). The experiment was conducted according to the manufacturer’s protocol. In brief, 250 ng RNA per sample were amplified, transcribed to cDNA, fragmented and subsequently labeled with Biotin.
|
| |
|
| Hybridization protocol |
Array hybridization was performed at 45°C for 16-18h in the Affymetrix GeneChip® Hybridization Oven 640, arrays were subsequently washed in the Fluidics Station 450.
|
| Scan protocol |
Arrays were scanned on the GeneChip scanner 3000 7G.
|
| Description |
Gene expression data from CLL sample
|
| Data processing |
Raw Affymetrix Human Exon array (HuEx-1_0-st-v2) data files have been normalized using the RMA algorithm using aroma.affymetrix
|
| |
|
| Submission date |
Feb 14, 2019 |
| Last update date |
Feb 13, 2023 |
| Contact name |
Johannes Bloehdorn |
| E-mail(s) |
johannes.bloehdorn@gmail.com
|
| Organization name |
University of Ulm
|
| Street address |
Albert-Einstein-Allee 23
|
| City |
Ulm |
| ZIP/Postal code |
89081 |
| Country |
Germany |
| |
|
| Platform ID |
GPL5175 |
| Series (1) |
| GSE126595 |
Expression data from CLL patient samples investigated to define biologic heterogeneity. |
|
