|
| Status |
Public on Nov 24, 2021 |
| Title |
PMF7 |
| Sample type |
RNA |
| |
|
| Source name |
CD34+ cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow
genotype: JAK2V617F
age: 76
Sex: M
diagnosis: PMF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Blood and bone marrow mononuclear cells from MPN patients were isolated using Ficoll density gradient centrifugation. Enrichment of the CD34+ cell population was performed by magnetic cell separation (MACS) with the CD34 MicroBead Kit, human (Miltenyi). RNA was isolated using the RNeasy Micro Kit (QIAGEN).
|
| Label |
biotin
|
| Label protocol |
Total RNA was process with Affymetrix GeneChip WT Plus Reagent Kit.
|
| |
|
| Hybridization protocol |
Overnight hybridization of end-labelled cDNA was applied on the HTA 2.0 Human (Affymetrix) arrays for 16 hours, at 60 rpm, at 45ºC in a Hybridization Oven 645 (Affymetrix). Washing and staining of the arrays were done on an Affymetrix 450 Fluidics Station using the protocol FS450_0001.
|
| Scan protocol |
Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the manufacture manual
|
| Data processing |
Batch correction was applied using sva and Combat. Downstream analysis was performed in R. Data were normalized with signal space transformation (SST) in conjunction with robust multiple-array (RMA) average normalization method (SST-RMA) with Affymetrix Expression console.
|
| |
|
| Submission date |
May 07, 2021 |
| Last update date |
Nov 24, 2021 |
| Contact name |
Lin Gan |
| Organization name |
University Hospital Aachen
|
| Department |
IZKF
|
| Lab |
Genomics facility
|
| Street address |
Pauwelsstr. 30
|
| City |
Aachen |
| ZIP/Postal code |
52074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17586 |
| Series (1) |
| GSE174060 |
Gene expression data from CD34+ BMMCs/PBMCs from MPN patients vs. healthy controls |
|
