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Sample GSM434718 Query DataSets for GSM434718
Status Public on Jan 10, 2010
Title 24_MO4 GRA9n
Sample type RNA
 
Source name Peripheral blood mononuclear cells
Organism Homo sapiens
Characteristics cell type: Peripheral blood mononuclear cells
disease state: healthy donors at 9th month pregnancy
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 30, 2009
Last update date Jan 10, 2010
Contact name Raffaele A Calogero
E-mail(s) raffaele.calogero@unito.it
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 (2)
GSE17409 Pregnancy changes expression in peripheral blood mononuclear cells of healthy donors
GSE17449 Transcription signature of Multiple Sclerosis

Data table header descriptions
ID_REF
VALUE 24_MO4 GRA9n

Data table
ID_REF VALUE
1007_s_at 5.513881841
1053_at 5.990278435
117_at 6.596052623
121_at 6.657643015
1255_g_at 2.704150185
1294_at 8.07483261
1316_at 4.269565416
1320_at 2.949394911
1405_i_at 11.34376364
1431_at 2.948229019
1438_at 4.158107894
1487_at 6.750947601
1494_f_at 4.623986256
1598_g_at 6.402639833
160020_at 5.608441889
1729_at 8.005541685
177_at 4.245703036
1773_at 4.870272191
179_at 7.217946036
1861_at 5.534478028

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM434718.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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