|
| Status |
Public on May 21, 2011 |
| Title |
LSK BL6 Msi2Gt rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Sorted LSK cells from Msi2 null animals
|
| Organism |
Mus musculus |
| Characteristics |
marker phenotype: CD3e-,CD4-,CD5-,CD8a-,CD19-,CD45R/B220-,CD11b-,Gr1-,Ter119-,Sca1+,ckit+
marker phenotype short name: LSK
genotype: Msi2Gt/Gt
cell type: LSK
genetic background: C57/Bl6
|
| Growth protocol |
BM cells were pooled from 4 Msi2Gt/Gt females (aged 6-7 weeks) or 4 C57/Bl6 females (aged 6-7 weeks) and subjected to lineage depletion. Cells from each pool were stained with fluorochrome-labelled anti-c-Kit and anti-Sca-1 monoclonal antibodies to mark LSK cells (defined as Lineage- Sca-1+ c-kit+) and Kit+ (defined as Lineage-, Sca-1-, c-kit+) and sorted by FACS into PBS+5%FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were pelleted and RNA was extracted using the RNeasy Mini Kit (Qiagen) by the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
cDNA from 25 ng of RNA was transcribed with T7 RNA polymerase in the presence of Cy3-CTP to produce labelled cRNA using the standard Agilent labelling protocol.
|
| |
|
| Hybridization protocol |
The labelled cRNA was hybridized to the Agilent Whole Mouse Genome 4x44k 60-mer oligo microarray using stnadard Agilent protocol.
|
| Scan protocol |
The arrays were scanned on an Agilent G2565CA microarray scanner at 110% PMT and 5 μm resolution.
|
| Data processing |
Intensity data was extracted using the Feature Extraction v 10.7.3.1 software (Agilent) and corrected for background noise using the normexp method [Ritchie ME etal. 2007. Bioinformatics]. To assure comparability across samples we use quantile normalization [Bolstad, B. (2001). Unpublished manuscript http://bmbolstad.com/stuff/qnorm.pdf].
|
| |
|
| Submission date |
May 20, 2011 |
| Last update date |
May 21, 2011 |
| Contact name |
Eric M. Kallin |
| E-mail(s) |
eric.kallin@crg.es
|
| Organization name |
Center for Genomic Regulation
|
| Department |
Differentiation and Cancer
|
| Lab |
Thomas Graf
|
| Street address |
C/ Dr. Aiguader, 88
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL10333 |
| Series (1) |
| GSE29432 |
Musashi 2 is a regulator of the hematopoietic stem cell compartment identified by a retroviral insertion screen and knockout mice |
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