|
| Status |
Public on Jun 18, 2015 |
| Title |
412-primagraft_CHZ treatment |
| Sample type |
RNA |
| |
|
| Source name |
05-412
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary graft 05-412
treatment: CHZ
replicate: na
cell type: splenocyte
|
| Treatment protocol |
MHH-CALL4 cells cultured at 1 x 10^6 cells/mL were treated with vehicle (DMSO), CHZ868 (500nM), dexamethasone (250nM), or CHZ868 + dexamethasone combination for 12 hours. Experiment was performed in triplicate.
Primary human xenografts 05-412, 05-440, and 05-537 were treated in vivo with vehicle, CHZ868 (30mg/kg/day), dexamethasone (1mg/kg/day), or CHZ868 + dexamethasone combination for three days and then sacrificed. Transcriptional profiling was performed on unselected splenocytes.
|
| Growth protocol |
MHH-CALL4 cells were cultured in RPMI-1640 with 20% FBS, 1% penicillin-streptomycin, and 2mM L-alanyl-L-glutamine.
05-412, 05-440, and 05-537 CRLF2+ patient-derived xenografts were generated in NSG mice by tail vein injection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol followed by purification on a Qiagen RNeasy column.
|
| Label |
biotin
|
| Label protocol |
cRNA was biotinylated according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.
|
| Scan protocol |
GCS3000 (Affymetrix)
|
| Data processing |
The raw cel files were converted into probeset-specific expression values using Affymetrix RMA summarization method using Brainarray cdf annotations (hta20hsensgcdf_18.0.0.cdf, version 18) as implemented in the BioConductor package affy (Gentleman et al., 2004). Ensemble IDs were converted to HUGO gene symbols using the biomaRt package and collapsed by their median. Cell line and primagraft data were profiled seperatly and therefore treated as different batches.
|
| |
|
| Submission date |
Sep 24, 2014 |
| Last update date |
Jun 18, 2015 |
| Contact name |
Loretta Li |
| E-mail(s) |
loretta_li@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Weinstock Lab
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL19198 |
| Series (1) |
| GSE61696 |
Type II JAK2 Inhibitor NVP-CHZ868 is Active in Vitro and in Vivo Against JAK2-Dependent B-cell Acute Lymphoblastic Leukemias |
|
