|
| Status |
Public on Jul 15, 2011 |
| Title |
Sox17-expressing_CD48+LSK_Rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Sox17-expressing CD48+LSK hematopoietic progenitors isolated from primary recipients that were reconstituted with MSCV-Sox17 retrovirus infected adult bone marrow cells 12 weeks earlier
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CD48+Lineage-Sca1+ckit+ bone marrow hematopoietic progenitors
strain: C57BL/6
developmental stage: Adult
treatment: MSCV-Sox17 retrovirus infected
|
| Treatment protocol |
The isolated hematopoietic stem/progenitor cells were processed without treatment.
|
| Growth protocol |
3 independent replicates of uncultured 10,000 E16.5 fetal liver HSCs, 10,000 fetal liver CD48+LSK cells, 10,000 adult bone marrow HSCs, 10,000 adult bone marrow CD48+LSK cells and 10,000 Sox17-expressing CD48+LSK cells isolated from primary recipients 12 weeks after transplantation of MSCV-Sox17-infected bone marrow cellswere double-sorted into Trizol (Invitroen)
|
| 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 25˚C, followed by 15 min at 37˚C 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 Sox17-expressing CD48+LSK hematopoietic progenitors isolated from primary recipients that were reconsituted with MSCV-Sox17 retrovirus infected adult bone marrow cells 12-weeks earlier
Sox17_CD48+LSK3.CEL
|
| 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 |
Jul 06, 2011 |
| Last update date |
Jul 15, 2011 |
| Contact name |
Shenghui He |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Michigan
|
| Department |
Life Science institute
|
| Lab |
Sean Morrison
|
| Street address |
210 Washtenaw Avenue, 5258 LSI
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (2) |
| GSE30444 |
Retroviral Sox17 over-expression adult hematopoietic stem/progenitor cells microarray |
| GSE30446 |
Transcription factor SOX17 overexpression in hematopoietic stem cells |
|
