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Sample GSM1227399 Query DataSets for GSM1227399
Status Public on Nov 04, 2013
Title bone_marrow_TA+_B-ALL_pat1
Sample type RNA
 
Source name TEL-AML1 positive B-ALL
Organism Homo sapiens
Characteristics disease state: TEL-AML1 positive B-ALL
tissue: bone marrow
timepoint of sample collection: diagnosis
Growth protocol Bone marrow samples of TEL-AML1 positive patients were collected at time of diagnosis. After isolation of mononuclear cells, samples were frozen and stored in the gas-phase of liquid nitrogen until RNA isolation. Peripheral blood samples were taken from TEL-AML1 negative healthy donors. The isolated mononuclear cells were sorted for CD19+ cells and stored until RNA isolation.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol (Invitrogen) according to manufacturer's protocol. Quality of the RNA was checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies).
Label Cy3
Label protocol 10 ng of each total RNA sample was used for linear T7-based amplification. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).
 
Hybridization protocol The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven.
Scan protocol Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies).
Description TEL-AML1 expression
Data processing The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver® gene expression data analysis system (Rosetta Biosoftware).
 
Submission date Sep 10, 2013
Last update date Nov 05, 2013
Contact name Pablo Landgraf
E-mail(s) pablo.landgraf@gmx.de
Organization name Heinrich-Heine University Düsseldorf
Department Clinic of Pediatric Oncology, Hematology and Clinical Immunology
Street address Moorenstraße 5
City Düsseldorf
ZIP/Postal code 40225
Country Germany
 
Platform ID GPL13607
Series (2)
GSE50734 TEL-AML1 (ETV6-RUNX1) in B-cells and leukemia (part 5)
GSE50736 TEL-AML1 (ETV6-RUNX1) in B-cells and leukemia

Data table header descriptions
ID_REF
VALUE All samples were labeled with Cy3. The ratio experiments are designated as control versus sample experiments (automated output of the Resolver® system). The ratios are always calculated by dividing sample signal intensity through control signal intensity.

Data table
ID_REF VALUE
4 7.954729
5 6.196281
6 2.244643
7 10.434067
8 78.985514
9 0.069284
10 1.053597
11 0.069215
12 53.719869
13 38.472220
14 12.368644
15 104.437912
16 0.068958
17 1.274581
18 0.119792
19 0.068729
20 26.076668
21 14.805943
24 1.614409
25 22.914432

Total number of rows: 58717

Table truncated, full table size 866 Kbytes.




Supplementary file Size Download File type/resource
GSM1227399_US22502695_252800414355_S01_GE1_107_Sep09_1_3.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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