|
| Status |
Public on Nov 07, 2012 |
| Title |
Mouse4_KO_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
primary cells from bone marrow, HSC-enriched, BAP1 KO
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype: BAP1 KO
cell type: HSC-enriched lineage-ScaI+Kit+ cells
mouse identifier: 4
|
| Growth protocol |
These data were collected with only primary cells isolated from BAP1 WT and KO mice. The mice were injected with tamoxifen to induce systemic deletion of BAP1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy Mini Kit as per the manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
RNA was converted to double-stranded cDNA and amplified using in vitro transcription that included amino-allyl UTP. The aRNA product was subsequently conjugated with Cy5™ NHS ester (GEH Lifesciences).
|
| |
|
| Hybridization protocol |
Fragmented aRNA was hybridized at 42°C overnight using the HybBag mixing system with 1X OneArray® Hybridization Buffer (Phalanx Biotech), 10 mg/ml sheared salmon sperm DNA (Promega), at a concentration of 25 mg/ml labeled target. After hybridization, the arrays were washed according to the OneArray® protocol.
|
| Scan protocol |
Raw intensity signals for each microarray were captured using a Molecular Dynamics™ Axon 4100A scanner, measured using GenePixPro™ Software, and stored in GPR format.
|
| Description |
K4_H011
|
| Data processing |
Expression summary values for all probes were obtained by doing background correction and quantile normalization with the 'limma' package from Bioconductor. Statistical analyses of differentially expressed genes were performed using linear models and empirical Bayes moderated statistics as implemented in the 'limma' package. Significant genes were defined as those with Benjamini-Hochberg adjusted p-values < 0.1 and fold changes > 2.
|
| |
|
| Submission date |
Aug 31, 2012 |
| Last update date |
Nov 08, 2012 |
| Contact name |
Jinfeng Liu |
| E-mail(s) |
liu.jinfeng@gene.com
|
| Organization name |
Genentech Inc.
|
| Department |
Bioinformatics and Computational Biology
|
| Street address |
1 DNA Way, MS93
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL13692 |
| Series (1) |
| GSE40541 |
Transcriptome profiles of hematopoietic lineages from BAP1 WT and KO mice |
|
