|
| Status |
Public on Jun 29, 2017 |
| Title |
199 |
| Sample type |
RNA |
| |
|
| Source name |
Newly diagnosed T-ALL patient (bone marrow)
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: T-ALL
tissue: bone marrow
|
| Treatment protocol |
COG study 9404/0434 (diagnostic samples)
|
| Growth protocol |
Derived from bone marrow in newly diagnosed T-ALL patients
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instruction
|
| Label |
Biotin
|
| Label protocol |
Biotin-labed cRNA from 1 micrograms of tissue using a one-step method usng Affymetrix technical approach
|
| |
|
| Hybridization protocol |
15 ug aliquots of fragmented, labelled cRNA were hybridized to the U133 Plus 2 chip (Affymetrix)
|
| Scan protocol |
Affymerix microarray scanner (Hewlett Packard), gene fluorescence was captured using GeneChip software.
|
| Description |
Gene expression data from primary T-ALL samples at diagnosis
sample name: 199
COG study 0434
|
| Data processing |
The Robust Multi-array Average (RMA) algorithm was used to generate and normalize signal intensities (Bioconductor/R). Scale factor < 40; GAPDH M33197 3′ intensity > 15 000; and GAPDH M33197 3′/5′ ratio < 3 were applied as array experimental quality parameters. From 54,675 genes and expressed sequence tags, we selectively filtered out probes for gender, globins, and internal controls, and corrected for batch effects using z-score transformations.
|
| |
|
| Submission date |
Jul 06, 2015 |
| Last update date |
Nov 14, 2018 |
| Contact name |
Ksenia Matlawska |
| E-mail(s) |
[email protected]
|
| Phone |
5052726177
|
| Organization name |
University of New Mexico
|
| Department |
Pediatrics
|
| Lab |
BRF 140
|
| Street address |
915 Camino de Salud
|
| City |
Albuquerque |
| State/province |
NM |
| ZIP/Postal code |
87111 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE70536 |
Microarray analyses of T-ALL (COG study) |
| GSE77741 |
Analyses of T-ALL (COG study) |
|
| Relations |
| Reanalyzed by |
GSE122511 |
