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Sample GSM936720 Query DataSets for GSM936720
Status Public on Dec 20, 2012
Title PBMC_P2-0w_rep1
Sample type RNA
 
Source name MDE_PBMC_1 wk
Organism Homo sapiens
Characteristics status: major depressive episode (MDE)
gender: female
age: 58
treatment: Duloxetine, Mirtazapine, Lithium
hamilton depression rating scale with 17 items (hdrs-17): 27
sample collection: 1st week (during a severe episode of depression)
Extracted molecule total RNA
Extraction protocol 8-10ml venous peripheral blood from fasting patients and healthy controls were collected during 7am and 9am. PBMCs were separeted by Ficoll gradient centrifugation.Total RNA was isolated using the mirVanai Kit (Ambion) according to manufacturer's recommendation. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
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 Gene expression of MDE PBMCs
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 using limma R/bioconductor package (v.2.16.4).
 
Submission date May 24, 2012
Last update date Dec 20, 2012
Contact name El Chérif Ibrahim
E-mail(s) el-cherif.ibrahim@univ-amu.fr
Phone +33 (0)4 91 69 89 56
Fax +33 (0)4 91 69 89 20
Organization name Aix Marseille Université-CNRS
Department CRN2M-UMR7286
Street address Bd Pierre Dramard
City MARSEILLE
ZIP/Postal code 13015
Country France
 
Platform ID GPL13607
Series (1)
GSE38206 Transcription profiling of major depression peripheral blood mononuclear cells (PBMCs) at clinical remission compared to severe acute state

Data table header descriptions
ID_REF
VALUE quantile normalized

Data table
ID_REF VALUE
1 15.0801353742326
2 4.9723057852735
3 4.69418072000962
4 8.77149515278348
5 5.67938993880447
6 5.85379020315158
7 7.61326060831076
8 10.5061192522231
9 4.97199446649846
10 5.59237661038411
11 4.96912218676163
12 12.4038574621438
13 9.34594146256124
14 8.70439218547542
15 6.43126807526191
16 5.71115832573385
17 7.05586117367187
18 5.097124879665
19 5.2663959484044
20 8.02554070864088

Total number of rows: 62976

Table truncated, full table size 1394 Kbytes.




Supplementary file Size Download File type/resource
GSM936720_US83700202_252800413017_S01_GE1_107_Sep09_1_2.txt.gz 12.2 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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