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Sample GSM434512 Query DataSets for GSM434512
Status Public on Jan 10, 2010
Title VC1 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

Data table
1007_s_at 5.412763332
1053_at 5.833284943
117_at 7.727201477
121_at 6.990258683
1255_g_at 2.474572498
1294_at 8.066095118
1316_at 4.4540144
1320_at 3.175358469
1405_i_at 10.49126115
1431_at 3.095542939
1438_at 4.093939702
1487_at 6.649610246
1494_f_at 4.708659339
1598_g_at 6.56677145
160020_at 5.754071637
1729_at 8.093570347
177_at 4.250868771
1773_at 5.20179124
179_at 7.89232527
1861_at 5.268480762

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.

Supplementary file Size Download File type/resource
GSM434512.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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