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Sample GSM936747 Query DataSets for GSM936747
Status Public on Dec 20, 2012
Title PBMC_C6-8w_rep1
Sample type RNA
 
Source name Control_PBMC_8 wk
Organism Homo sapiens
Characteristics status: control
gender: male
age: 44
treatment: No treatment
sample collection: 8 weeks later after clinical remission
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 control 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 15.4209004141726
2 5.12506085184129
3 4.9942541986575
4 9.5848046738371
5 5.88375421175972
6 5.8394825352082
7 7.84347538592451
8 10.1191031624712
9 5.1118119243722
10 5.28952817343896
11 5.15746282131458
12 12.1460402465675
13 9.19275605975221
14 8.55733061043153
15 5.88853368983368
16 5.24317127901239
17 6.74278629388726
18 4.93514470141819
19 5.06222497223638
20 8.1600624446413

Total number of rows: 62976

Table truncated, full table size 1394 Kbytes.




Supplementary file Size Download File type/resource
GSM936747_US83700202_252800413016_S01_GE1_107_Sep09_1_4.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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