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Sample GSM1242456 Query DataSets for GSM1242456
Status Public on Oct 07, 2014
Title A612b_20_RAV19_1uM_Sunitinib_GF
Sample type RNA
 
Source name brain tumor initiating cells (BTIC)
Organism Homo sapiens
Characteristics cell type: brain tumor initiating cells (BTIC)
treatment: Sunitinib
gf: yes
btic culture: BTIC_8
treatment response of glioma in vitro_proliferation.score: 0.567
treatment response of glioma in vitro_proliferation.label: strong inhibition
treatment response of glioma in vitro_migration.score: 0.809
treatment response of glioma in vitro_migration.label: moderate inhibition
Treatment protocol Cells were cultured in growth factor free medium for 16 hours prior to treatment. After starvation, cells were treated with 1 µM Sunitinib in the treatment groups or 0.00025 % DMSO in the control groups either with or without supplementation of recombinant growth factors PDGF-A/B and VEGFA (25 ng/ml) for 6 hours before harvest.
Growth protocol BTICs were cultured in stem-cell permissive RHB-A media (Stem Cell, Cambridge, UK) supplemented with 20 ng/ml of each human recombinant epidermal growth factor (EGF; R&D Systems, Minneapolis, USA) and human recombinant basic fibroblast growth factor (FGF; Peprotech, Hamburg, Germany).
Extracted molecule total RNA
Extraction protocol Cells were washed twice with ice-cold PBS and harvested in RLT-lysis buffer (provided in the RNeasy Kit, Qiagen, Hilden, Germany) for subsequent RNA-extraction
Label biotin
Label protocol cRNA and ssDNA were prepared from 0.3 µg totalRNA according to the Ambion WT Expression Kit manual. Fragmentation and terminal biotinylation were performed using the Affymetrix Terminal Labeling Kit.
 
Hybridization protocol 3 μg of labelled products were hybridized, washed and stained in an Affymetrix GeneTitan system.
Scan protocol Arrays were scanned in an Affymetrix GeneTitan system.
Data processing Raw intensities were quantile normalized and summarized with the RMA (Robust Multichip Average) expression measure described in Irizarry et al, Biostatistics (2003)
For the final analysis, only those features were used that could be mapped to EntrezIDs.
 
Submission date Sep 30, 2013
Last update date Oct 08, 2014
Contact name Christian W Kohler
E-mail(s) [email protected]
Organization name University of Regensburg
Department Institute of Functional Genomics
Lab Statistical Bioinformatics
Street address Am BioPark 9
City Regensburg
State/province Bavaria
ZIP/Postal code 93053
Country Germany
 
Platform ID GPL11532
Series (1)
GSE51305 Gene expression profiles of Sunitinib-treated but not untreated short-term serum-free cultures predict treatment response of human high-grade gliomas in vitro

Data table header descriptions
ID_REF
VALUE RMA processed data is on log2 scale

Data table
ID_REF VALUE
7892501 4.05827637415014
7892502 4.33106413037791
7892503 2.33367371672475
7892504 6.34145630212585
7892505 2.34813448961471
7892506 4.46155657583397
7892507 3.88096752382748
7892508 6.67558400374785
7892509 10.0644731664638
7892510 5.14179223784107
7892511 3.56298310736083
7892512 4.15883367574421
7892513 3.67598858425104
7892514 10.3021268410706
7892515 8.0524844624932
7892516 2.38221632340893
7892517 6.39193940967226
7892518 3.02453428444607
7892519 4.09448597560543
7892520 6.956650752026

Total number of rows: 33297

Table truncated, full table size 809 Kbytes.




Supplementary file Size Download File type/resource
GSM1242456_A612b_20_RAV19_1uM_Sunitinib_GF.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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