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Sample GSM1094653 Query DataSets for GSM1094653
Status Public on Mar 07, 2014
Title 52_HR_S
Sample type RNA
Source name High responder, stimulated
Organism Homo sapiens
Characteristics subject: 52
disease status: multiple sclerosis (MS)
gender: male
age: 33
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 0.603487687
A_19_P00315459 5.229117083
A_19_P00315482 0.961002399
A_19_P00315492 3.031013092
A_19_P00315493 3.998516976
A_19_P00315502 1.531844562
A_19_P00315506 4.72199806
A_19_P00315518 0.877295344
A_19_P00315519 0.905863616
A_19_P00315524 7.840161775
A_19_P00315528 6.077610358
A_19_P00315529 6.22117029
A_19_P00315538 0.717487302
A_19_P00315541 0.710965091
A_19_P00315543 0.698000574
A_19_P00315550 3.142786205
A_19_P00315551 4.621118673
A_19_P00315554 0.623245095
A_19_P00315581 6.238765994
A_19_P00315583 2.485787176

Total number of rows: 35649

Table truncated, full table size 877 Kbytes.

Supplementary file Size Download File type/resource
GSM1094653_US91203659_253949410545_S01_GE1_107_Sep09_2_1.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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