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Sample GSM1094649 Query DataSets for GSM1094649
Status Public on Mar 07, 2014
Title 34_HR_S
Sample type RNA
Source name High responder, stimulated
Organism Homo sapiens
Characteristics subject: 34
disease status: multiple sclerosis (MS)
gender: male
age: 35
natalizumab responder type: high
tissue: whole blood
cell type: CD4+ T cells
treatment: none
Treatment protocol PBMCs were collected from 8 high responders (HR) and 8 low responders (LR) to natalizumab treatment and were stimulated with anti-CD3/-CD28 antibodies (0.1µg/mL, R&D Systems, Minneapolis, MN, USA), with or without addition of natalizumab (50µg/mL) and cultured for 48h.
Extracted molecule total RNA
Extraction protocol Total CD4+ T cells were enriched by MACS negative sorting (Miltneyi Biotec, Auburn, CA, USA). Total RNA was extracted using TRIreagent (Cincinnati, OH, USA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 15ng total RNA using a Low Input Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a total volume of 25ul following the manufacturer's instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides.
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. 24 samples were analyzed using the GPL16083 Platform, and 8 were analyzed using the GPL16705 Platform. Probes not detectable on either the GPL16083 or GPL16705 Platform were excluded. In addition, only probes common to both Platforms are presented. The raw data was extracted using GeneSpring GX software and was quantile normalized using the limma package in the R program. Batch effects were normalized using ComBat.
Submission date Mar 07, 2013
Last update date Mar 07, 2014
Contact name Hui Wang
Organization name Xuzhou Medical University
Street address 209 Tongshan Rd
City Xuzhou
State/province Jiangsu
ZIP/Postal code 224001
Country China
Platform ID GPL17077
Series (2)
GSE44964 Integrated genomic and prospective clinical studies show the importance of modular pleiotropy for disease susceptibility, diagnosis and treatment (dataset 2)
GSE44966 Integrated genomic and prospective clinical studies show the importance of modular pleiotropy for disease susceptibility, diagnosis and treatment

Data table header descriptions
VALUE Quantile- and ComBat-normalized signal intensity (natural log transformed)

Data table
A_19_P00315452 1.000937081
A_19_P00315459 3.716311552
A_19_P00315482 0.768357829
A_19_P00315492 2.130756194
A_19_P00315493 3.928991124
A_19_P00315502 0.671202543
A_19_P00315506 5.254094314
A_19_P00315518 0.80235279
A_19_P00315519 0.772255167
A_19_P00315524 7.433141811
A_19_P00315528 5.309081564
A_19_P00315529 5.159930008
A_19_P00315538 1.49164118
A_19_P00315541 1.390827702
A_19_P00315543 2.112790273
A_19_P00315550 3.208240427
A_19_P00315551 4.426760747
A_19_P00315554 1.606635179
A_19_P00315581 5.633413983
A_19_P00315583 2.688279645

Total number of rows: 35649

Table truncated, full table size 877 Kbytes.

Supplementary file Size Download File type/resource
GSM1094649_US91203659_253949410545_S01_GE1_107_Sep09_1_1.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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