|
| Status |
Public on Feb 01, 2012 |
| Title |
BM_Rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Whole bone marrow cells from wild-type mice.
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype: wild type
age: young adult
cell type: Whole bone marrow cells
|
| Growth protocol |
5,000 bone marrow Scf-GFP+ cells from Scf-GFP knockin heterozygous mice were double-sorted into Trizol (Invitroen). 5,000 whole bone marrow cells from wild-type mice were sorted into Trizol (Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol with 25 µg/ml linear acrylamide (Ambion). The extracted RNA (10 µl volume) was treated with 2 Units of RNase-free recombinant DNase I (Ambion) for 15 min at 25C, followed by 15 min at 37C to remove any contaminating genomic DNA. The DNA-free RNA samples were purified using the RNA Clean & Concentrator™-5 from Zymo Research and eluted in 10 µl of nuclease-free water. Purified RNA was reverse transcribed and amplified using the WT-Ovation™ Pico RNA Amplification system (NuGEN Technologies) following the manufacturer's instructions. Sense strand cDNA was generated using WT-Ovation™ Exon Module (NuGEN).
|
| Label |
biotin
|
| Label protocol |
cDNA was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN).
|
| |
|
| Hybridization protocol |
2.5µg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 1.0 microarrays.
|
| Scan protocol |
The chips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.
|
| Description |
Gene expresion data from whole bone marrow cells isolated from young adult wild type mice
|
| Data processing |
Data was analyzed using the limma, oligo and affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.
|
| |
|
| Submission date |
Oct 21, 2011 |
| Last update date |
Feb 01, 2012 |
| Contact name |
Lei Ding |
| Organization name |
Columbia University Medical Center
|
| Street address |
630 West 168 ST, P&S, room 7-513
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE33158 |
Scf-GFP+ cells from the bone marrow and whole bone marrow microarray |
|
