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Sample GSM1564780 Query DataSets for GSM1564780
Status Public on Dec 12, 2016
Title SS_P4 cells_SAHA+MitA_rep.1
Sample type RNA
 
Source name SS cells_SAHA+MitA_24 h
Organism Homo sapiens
Characteristics subject status: Sézary Syndrome (SS) patient
gender: male
age (yrs): 39
cell type: peripheral blood tumor cells
tumor stage: III
treatment: ECPx32/Roferon
% cd3+ in pbmc: 95
cd4+/cd8+ ratio: 70
Treatment protocol Expanded cells were treated, or not, with SAHA (2.6 µM) and MitA (223 nM) for 24 h.
Growth protocol PBMC were collected from 4 Sézary Syndrome (SS) patients and were put in culture without prior further purification because of the high percentage of T lymphocytes and the great majority of CD4+ among them. Cells were expanded for seven days in RPMI medium in the presence of IL-7 (10 ng/ml) and anti-CD28 (mAb ascites 1/400).
Extracted molecule total RNA
Extraction protocol Cells were recovered after drug treatment and RNA was extracted with Qiagen RNeasy® mini Kit. On column DNA digestion was done with Qiagen Rnase-free Dnase set.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 600 ng of Cy3-labelled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.
Description P4_1_S.M
US83700202_252800415433_S01_GE1_107_Sep09_1_4
Data processing The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization.
 
Submission date Dec 12, 2014
Last update date Dec 12, 2016
Contact name CHELBI RABIE
Organization name CIML
Street address Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, Case 906, 13288 Marseille cedex 9
City MARSEILLE
ZIP/Postal code 13009
Country France
 
Platform ID GPL13607
Series (1)
GSE64119 Insights into the combined action of SAHA (vorinostat) and Mithramycin A in Sézary cells through gene expression profiling

Data table header descriptions
ID_REF
VALUE log2 normalized

Data table
ID_REF VALUE
1 15.6531506560774
2 5.26038424847063
3 5.22510348580057
4 10.1877497894714
5 6.08500459707549
6 6.58123498970384
7 8.626835141336
8 8.76531770058526
9 5.39628994077279
10 5.84026168102571
11 5.31990575627616
12 10.5032564180857
13 7.89567606170859
14 7.09493352413437
15 6.87338061741673
16 5.1275172391396
17 7.55485149632648
18 5.41630987344626
19 5.58771255530214
20 9.31184028654302

Total number of rows: 62976

Table truncated, full table size 1396 Kbytes.




Supplementary file Size Download File type/resource
GSM1564780_US83700202_252800415433_S01_GE1_107_Sep09_1_4.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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