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Sample GSM1015915 Query DataSets for GSM1015915
Status Public on Oct 01, 2013
Title CMLbonemarrow_classic 20
Sample type RNA
 
Source name CML_bone marrow_classic
Organism Homo sapiens
Characteristics gender: female
disease type: chronic myeloid leukemia (CML)
translocation type: classic t(9;22) rearrangement
tissue: bone marrow
cell type: total white blood cells
Treatment protocol Total white blood cells were isolated from CML BM samples by hypotonic red cell lysis, washed, transferred into a guanidinium isothiocyanate-containing buffer, and stored at -80°C.
Extracted molecule total RNA
Extraction protocol Whole RNA was extracted by ultracentrifugation in caesium chloride density gradient. RNA quality was determined using the 2100 Bioanalyzer; only cellular samples of high quality characterized by RNA integrity numbers ranging from 8 to 10 were selected.
Label Cy3
Label protocol Twenty-five nanograms of each sample were labeled using the Low Input Quick Amp Labeling kit (Agilent).
 
Hybridization protocol Labeled cRNAs were hybridized for 17 hours at 65°C and 10 RPM on the Agilent SurePrint G3 Human GE 8x60K Microarray slide (Agilent Technologies) using the Agilent’s Microarray Hybridization Oven.
Scan protocol Slides were scanned using the High-Resolution Microarray C Scanner (Agilent Technologies) according to the Agilent_G3_GX_1Color protocol.
Description SAMPLE 20
Data processing Scanned images were processed using the Agilent Feature Extraction software (v10.7.3.1), raw data were quantile normalized and differentially expressed genes were selected by unpaired t-test and Multiple Testing Correction of Benjamini-Hochberg, considering as statistically significant those presenting a p-value less than 0.05 and a fold-change equal or higher than 2.
 
Submission date Oct 05, 2012
Last update date Oct 01, 2013
Contact name Francesco Albano
E-mail(s) francesco.albano@uniba.it
Organization name University of Bari
Department D.E.T.O.
Lab Hematology Section
Street address P.zza G. Cesare, 11
City Bari
ZIP/Postal code 70124
Country Italy
 
Platform ID GPL14550
Series (1)
GSE41375 Gene expression profiling of chronic myeloid leukemia with variant t(9;22) reveals a different signature from cases with classic translocation.

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner -1.4139519
DarkCorner -0.021659613
A_23_P326296 -0.2834649
A_24_P287941 0.10693216
A_24_P325046 0.357275
A_23_P200404 0.80502987
A_19_P00800513 -0.64081717
A_23_P15619 -0.02215445
A_33_P3402354 -0.9632089
A_33_P3338798 0.41033053
A_32_P98683 -1.0320325
A_23_P137543 -0.15277147
A_19_P00803040 -0.49725866
A_23_P117852 0.8775978
A_33_P3285585 -0.0031604767
A_24_P328231 0.18751264
A_33_P3415668 -0.024264216
A_23_P73609 -0.04993546
A_24_P186124 -0.19646263
A_23_P369983 -0.28612423

Total number of rows: 42545

Table truncated, full table size 1046 Kbytes.




Supplementary file Size Download File type/resource
GSM1015915_US10123792_252800415783_S01_GE1_107_20.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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