|
| Status |
Public on Nov 14, 2005 |
| Title |
B-ALL-37-BM-unsorted |
| Sample type |
RNA |
| |
|
| Source name |
B-ALL patient 37, bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
biological source:
homo sapiens, childhood ALL patient (female, aged 15.1 years), bone marrow taken prior to treatment, leukocyte isolation without enrichment for malignant blasts.
|
| Treatment protocol |
(BFM2000 treatment protocol)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
|
| Label |
R-Phycoerythrin
|
| Label protocol |
The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
|
| |
|
| Hybridization protocol |
On rotation (60 rpm) hybridization at 45C for 16 hours
|
| Scan protocol |
Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
|
| Description |
biological source:
homo sapiens, childhood ALL patient (female, aged 15.1 years), bone marrow taken prior to treatment, leukocyte isolation without enrichment for malignant blasts.
|
| Data processing |
Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
|
| |
|
| Submission date |
Jun 09, 2005 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Johannes Rainer |
| E-mail(s) |
johannes.rainer@eurac.edu
|
| Organization name |
Eurac Researc
|
| Department |
Institute for Biomedicine
|
| Lab |
Biomedical Informatics
|
| Street address |
Via A. Volta 21
|
| City |
Bolzano |
| ZIP/Postal code |
39100 |
| Country |
Italy |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE2842 |
Additional systems to Prednisolone treated childhood ALL samples |
|
| Relations |
| Reanalyzed by |
GSE64985 |
| Reanalyzed by |
GSE119087 |
