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Sample GSM1511405 Query DataSets for GSM1511405
Status Public on Jun 18, 2015
Title MHH-CALL4_Vehicle treatment - replicate 1
Sample type RNA
 
Source name MHH-CALL4
Organism Homo sapiens
Characteristics cell line: MHH-CALL4
treatment: Vehicle
replicate: 1
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

Data table header descriptions
ID_REF
VALUE log 2 transformed RMA normalized expression values.

Data table
ID_REF VALUE
ENSG00000000003_at 3.969212241
ENSG00000000005_at 4.052670884
ENSG00000000419_at 9.74234857
ENSG00000000457_at 7.203433613
ENSG00000000460_at 7.194542919
ENSG00000000938_at 6.920466844
ENSG00000000971_at 3.435791457
ENSG00000001036_at 4.367040853
ENSG00000001084_at 6.537364901
ENSG00000001167_at 9.486532394
ENSG00000001460_at 5.169316232
ENSG00000001461_at 6.724575341
ENSG00000001497_at 8.567645851
ENSG00000001561_at 3.21000087
ENSG00000001617_at 7.341583035
ENSG00000001626_at 4.290518667
ENSG00000001629_at 8.772347468
ENSG00000001631_at 8.578307756
ENSG00000002016_at 7.563772561
ENSG00000002079_at 6.016032253

Total number of rows: 35752

Table truncated, full table size 1078 Kbytes.




Supplementary file Size Download File type/resource
GSM1511405_1_M4_Veh_1.CEL.gz 25.6 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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