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Sample GSM434518 Query DataSets for GSM434518
Status Public on Jan 10, 2010
Title 21 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 21 preN

Data table
1007_s_at 5.661374199
1053_at 6.308655767
117_at 7.074269539
121_at 7.153378319
1255_g_at 2.604410108
1294_at 7.762985234
1316_at 4.462627468
1320_at 3.077303903
1405_i_at 11.28883142
1431_at 3.07130307
1438_at 4.163856636
1487_at 6.638479908
1494_f_at 4.617074097
1598_g_at 6.715297359
160020_at 5.888829292
1729_at 8.074664239
177_at 4.01604232
1773_at 5.191964994
179_at 7.416390433
1861_at 5.235440386

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.

Supplementary file Size Download File type/resource
GSM434518.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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