|
| Status |
Public on Jun 02, 2009 |
| Title |
LSK_OP9-GFP_Rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Hematopoietic LSK cells plated on OP9-GFP stroma for 3 days
|
| Organism |
Mus musculus |
| Characteristics |
C57/Bl6
|
| Treatment protocol |
After 3 days of co-cultures, non-adherent cells were collected
|
| Growth protocol |
Prospectively purified bone marrow hematopoietic stem cells (LSK, defined as Lineage- Sca-1+ c-Kit+) from wild-type C57/Bl6 mice were co-cultured for 3 days on OP9-GFP, OP9-DL1 or OP9-DL1+CompoundE (gamma-secretase inhibitor: 1µM) stromal layers.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using Qiagen Rneasy Micro Kit following manufacturer's recommendation
|
| Label |
Biotin
|
| Label protocol |
For each condition, 25ng of RNA was amplified and labelled using the Ovation Biotin system (Nugen) following manufacturer's recommendations.
|
| |
|
| Hybridization protocol |
standard Affymetrix protocol
|
| Scan protocol |
standard Affymetrix protocol
|
| Description |
Gene expression data from LSK cells plated on OP9-GFP stroma for 3 days
|
| Data processing |
The ‘.CEL’ files from the MAS5 software were used as starting points for all analyses (3 replicates per condition). Data were analyzed using the R statistical package bioconductor and data quality assessed using functions in the Affy and AffyPLM packages. The GCRMA algorithm (ver. 2.4.1) was used to obtain normalized expression estimates. Genes that were selected for further analysis had probe sets for which the expression value was greater than 27(log2) (which in our study constitutes the average background reading for all probe sets) and a present flag call in at least 2 of 3 samples. To detect significant changes in the expression levels, two-sample Welch t-tests (parametric; assuming unequal variances; Benjamini and Hochberg step-up multiple testing correction at a False Discovery Rate <0.05) was applied to the resulting genes. The resulting mouse genes associated with Mouse Genome 430 2.0 GeneChip arrays were extracted via the NetAffx Gene Ontology Mining tool (Affymetrix).
|
| |
|
| Submission date |
Jun 09, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Thomas Mercher |
| E-mail(s) |
tmercher@rics.bwh.harvard.edu, ggilliland@rics.bwh.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Hematology
|
| Lab |
Dr. Gary Gilliland
|
| Street address |
1 blackfan circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE11723 |
Role of Notch signaling on hematopoietic stem cell differentiation |
|
| Relations |
| Reanalyzed by |
GSE119085 |
