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Sample GSM1511413 Query DataSets for GSM1511413
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

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

Data table
ID_REF VALUE
ENSG00000000003_at 3.74392128
ENSG00000000005_at 3.826501495
ENSG00000000419_at 9.020896747
ENSG00000000457_at 6.419910991
ENSG00000000460_at 7.094128292
ENSG00000000938_at 6.562610653
ENSG00000000971_at 6.108053616
ENSG00000001036_at 3.977030249
ENSG00000001084_at 5.141999349
ENSG00000001167_at 9.493154842
ENSG00000001460_at 5.461290819
ENSG00000001461_at 6.65859382
ENSG00000001497_at 8.055405469
ENSG00000001561_at 2.985404875
ENSG00000001617_at 6.982205106
ENSG00000001626_at 3.927967607
ENSG00000001629_at 7.94188612
ENSG00000001631_at 7.920618099
ENSG00000002016_at 7.448375641
ENSG00000002079_at 5.672218804

Total number of rows: 35752

Table truncated, full table size 1078 Kbytes.




Supplementary file Size Download File type/resource
GSM1511413_56_412_CHZ.CEL.gz 24.7 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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