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Sample GSM434523 Query DataSets for GSM434523
Status Public on Jan 10, 2010
Title 32 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 32 preN

Data table
1007_s_at 5.353641873
1053_at 6.193298271
117_at 6.422497069
121_at 6.828426453
1255_g_at 2.433432877
1294_at 7.998135225
1316_at 4.462047836
1320_at 3.112104203
1405_i_at 11.19915245
1431_at 3.378748786
1438_at 4.03056557
1487_at 6.607042138
1494_f_at 4.464397559
1598_g_at 6.48898018
160020_at 5.578157914
1729_at 8.082613045
177_at 4.101405574
1773_at 5.055016333
179_at 7.314373401
1861_at 5.515661458

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.

Supplementary file Size Download File type/resource
GSM434523.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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