|
| Status |
Public on Apr 30, 2015 |
| Title |
GMP_WT_1 |
| Sample type |
RNA |
| |
|
| Source name |
FACS-sorted GMP cells (WT)
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
transplanted with: WT bone marrow cells
tissue: bone marrow of recipient mice
cell type: FACS-sorted in vivo GMP cells (Lin-cKit+Sca1-CD16/32+CD150-)
arrayslide: 252800516543
subarray id: 1_1
|
| Treatment protocol |
N/A
|
| Growth protocol |
FACS-sorted in vivo GMP cells (Lin-cKit+Sca1-CD16/32+CD150-) were isolated from bone marrow of recipient mice one month after transplantation of WT bone marrow or splenic cells from two independent moribond Tet2-/-:AE leukemic mice (LeuA/AE1 or LeuB/AE3)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Allprep Micro Kit (Qiagen)
|
| Label |
Cy3
|
| Label protocol |
Biological triplicates were labeled and hybridized to Agilent SurePrint G3 Mouse GE 8x60K arrays according to manufacturers instructions
|
| |
|
| Hybridization protocol |
standard Agilent procedure
|
| Scan protocol |
standard Agilent procedure
|
| Description |
Gene expression data from in vivo FACS-sorted GMP cells isolated from secondary recipients transplanted with WT cells_Biological replicate 1
|
| Data processing |
Agilent microarrays were normalized using the RMA function from the Bioconductor affy package (Gautier et al., 2004). The normalized arrays were then background corrected using the normal+exponential convolution model with saddle-point approximation to maximum likelihood (Ritchie et al., 2007) and normalized between arrays by Cyclic Loess using the limma package implementation (Smyth and Speed, 2003). In the processed data file, spike-in and control probes were removed and the remaining probe list was collapsed based on unique identifiers to only retain the best probe (lowest p-value) for a given transcript. This yielded a final processed data file containing a total of 37877 rows.
|
| |
|
| Submission date |
Apr 29, 2015 |
| Last update date |
Apr 30, 2015 |
| Contact name |
Kasper Dindler Rasmussen |
| E-mail(s) |
[email protected]
|
| Organization name |
School of Life Sciences, University of Dundee
|
| Department |
Division of Molecular, Cellular, and Developmental Biology (MCDB)
|
| Street address |
Dow Street
|
| City |
Dundee |
| ZIP/Postal code |
DD1 5EH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL10787 |
| Series (2) |
| GSE59591 |
Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis |
| GSE68415 |
Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis [Agilent] |
|
