|
| Status |
Public on Jun 27, 2016 |
| Title |
GMPder_noDOX_48h_F6-6 |
| Sample type |
RNA |
| |
|
| Source name |
in vitro immortalized GMP der. -dox 48h, biological rep3
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: cells harvested from liquid medium
|
| Treatment protocol |
The samples were washed in PBS buffer, resuspended in 100 ul Pico Pure lysis buffer and frozen to -80°C until RNA isolation.
|
| Growth protocol |
The respective cells or tissue were collected as described above.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the Pico Pure extraction kit from Applied Biosystems (Catalog number KIT0204).
|
| Label |
biotin
|
| Label protocol |
19 ng of RNA in 5 ul volume was used for the Ovation Pico WTA System (NuGen) according to manufacturer's instructions to generate SPIA cDNA. 3 ug of SPIA cDNA was used to generate sense target cDNA with the WT Ovation Exon module according to manufacturer's instructions. 5.5 ug single-stranded DNA was fragmented and labelled using the Affymetrix GeneChip WT Terminal Labelling kit according to manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Following fragmentation, 2.75 ug of ssDNA were hybridized to Mouse Gene 1.0 GeneChips for 16 hours at 45 °C. Gene Chips were washed and stained at the Affymetrix Fluidics Station FS450.
|
| Scan protocol |
GeneChips were scanned using am Affymetrix GeneChip Scanner 3000.
|
| Data processing |
The data was analyzed using the affy and limma package of the statistical language R (version 3.1.1) in the Bioconductor environment.
|
| |
|
| Submission date |
Jan 28, 2015 |
| Last update date |
Jun 27, 2016 |
| Contact name |
Antoine Peters |
| E-mail(s) |
[email protected]
|
| Organization name |
Friedrich Miescher Institute for Biomedical Research (FMI)
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL6246 |
| Series (2) |
| GSE65382 |
MLL-AF9 Expression in Hematopoietic Stem Cells Drives a Highly Invasive AML Expressing EMT-Related Genes Linked to Poor Outcome [Microarray] |
| GSE65384 |
MLL-AF9 Expression in Hematopoietic Stem Cells Drives a Highly Invasive AML Expressing EMT-Related Genes Linked to Poor Outcome |
|
