|
| Status |
Public on Dec 21, 2012 |
| Title |
control rep2 |
| Sample type |
RNA |
| |
|
| Source name |
sorted GFP-positive cells
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
cell source: bone marrow cells
cell population: Lineage-depleted c-Kit+ Lin– cells
transduction: MSCV-IRES-GFP-empty
|
| Treatment protocol |
Experiment 1 (Samples 1-6): Bone marrow cells were harvested from 3x15 C57BL/6 mice, and differentiated cells were removed by incubation with rat antibodies against lineage antigens (CD3, CD4, CD8, Gr-1, B220, CD19, IL-7R, Ter119) followed by depletion with magnetic beads (Dynabeads, Invitrogen). Lineage-depleted cells were stained with APC-conjugated anti-c-Kit and PE-Cy5-conjugated goat anti-rat antibodies, and c-Kit+ Lin– cells were sorted using a BD FACSAria cell sorter (BD Biosciences). Cells were plated in RetroNectin-coated tissue culture dishes (Takara Bio) and transduced twice with pMSCV-Cdx2-IRES-GFP or pMSCV-IRES-GFP retroviral constructs. After 48 hours, GFP-positive cells were sorted using a BD FACSAria cell sorter.
Experiment 2 (Samples 7-10): Bone marrow cells isolated from C57BL/6 mice were transduced with pMSCV-Cdx2-IRES-GFP, and 8x10e5 GFP-positive cells were injected into lethally irradiated syngeneic recipient mice after 48 hours, followed by injection of 1x10e6 spleen cells from primary leukemic animals into sublethally irradiated secondary recipients. Spleen cells from secondary leukemic animals were harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen).
|
| Label |
Biotin
|
| Label protocol |
For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.
|
| |
|
| Hybridization protocol |
Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
|
| Scan protocol |
Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
|
| Description |
SAMPLE 2
Gene expression data from murine hematopoietic stem and progenitor cells
|
| Data processing |
The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed
|
| |
|
| Submission date |
Sep 17, 2012 |
| Last update date |
Dec 22, 2012 |
| Contact name |
Lars Bullinger |
| E-mail(s) |
lars.bullinger@charite.de
|
| Phone |
+49-30-450-553111
|
| Organization name |
Charité
|
| Department |
Hematology, Oncology and Tumorimmunology
|
| Street address |
Augustenburger Platz 1
|
| City |
Berlin |
| ZIP/Postal code |
13353 |
| Country |
Germany |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE40939 |
Leukemogenesis by CDX2 involves KLF4 repression and deregulated PPARgamma signaling. |
|
