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Sample GSM434520 Query DataSets for GSM434520
Status Public on Jan 10, 2010
Title 26 preN
Sample type RNA
Source name Peripheral blood mononuclear cells
Organism Homo sapiens
Characteristics cell type: Peripheral blood mononuclear cells
disease state: healthy
Extracted molecule total RNA
Extraction protocol PBMCs were isolated from edetic anticoagulated whole blood by centrifugation over LymphoprepTM separation medium (Axis-Shield, Oslo, Norway) and were subjected to RNA extraction using the TriReagent® as instructed by the manufacturer (Ambion, Austin, TX). The time delay from a blood draw to RNA extraction of PBMCs was about 30 minutes.
Label biotin
Label protocol Double strand cDNA was synthesized from 1 ug of total RNA using a cDNA Synthesis System (InvitroGen, Basel, Switzerland) with the T7-(T)24 primer. The in vitro-labeling kit (Enzo; Farmingdale, NY) was used to transcribe the cDNA into cRNA in the presence of Biotin-11-CTP and Biotin-16-UTP according to the instructions supplied with the kit.
Hybridization protocol Twelve ug fragmented cRNA was then used for hybridization. Hybridization and staining were performed as suggested by manufaturer.
Scan protocol Hybridized Arrays were scanned using an Affymetrix GeneChip 3000 scanner.
Description We conducted a genome-wide transcription analysis in peripheral blood mononuclear cells (PBMCs) from 14 women (9 MS patients and 5 normal controls) followed during their pregnancy. Samples were obtained before pregnancy and at the third, sixth, and ninth month of gestation. Findings were corroborated by real time RT-PCR in a larger cohort of MS patients (n=28) and healthy controls (n=11). Afterwards, we compared expression profiles of patients relapsing during pregnancy (n=23) with those of relapse-free patients (n=5).
Data processing GeneChip Operating Software (GCOS) (Affymetrix, Santa Clara, CA) was used to generate background-normalized image data (CEL files). Microarray quality controls and statistical validation was done using Bioconductor. The presence of hybridization/construction artifacts was evaluated with the fitPLM function (Bioconductor package affyPLM), and the probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of RMA (Robust Multichip Average) and normalization was done according to the quantiles method.
Submission date Jul 29, 2009
Last update date Jan 10, 2010
Contact name Raffaele A Calogero
Phone ++39 0116706454
Organization name University of Torino
Department Molecular Biotechnology Center
Lab Bioinformatics and Genomics Unit
Street address Via Nizza 52
City Torino
State/province To
ZIP/Postal code 10126
Country Italy
Platform ID GPL571
Series (3)
GSE17393 Transcription signature of Multiple Sclerosis in peripheral blood mononuclear cells.
GSE17409 Pregnancy changes expression in peripheral blood mononuclear cells of healthy donors
GSE17449 Transcription signature of Multiple Sclerosis

Data table header descriptions
VALUE 26 preN

Data table
1007_s_at 5.620011899
1053_at 6.347179622
117_at 7.125885457
121_at 7.232632886
1255_g_at 2.713514828
1294_at 7.940522701
1316_at 4.380271867
1320_at 2.984424498
1405_i_at 11.3011001
1431_at 3.098840216
1438_at 4.434377587
1487_at 6.727187574
1494_f_at 4.719906303
1598_g_at 6.700388572
160020_at 5.976833369
1729_at 8.276894818
177_at 4.093126331
1773_at 5.123414136
179_at 7.600525188
1861_at 5.305510617

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.

Supplementary file Size Download File type/resource
GSM434520.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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