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Sample GSM978835 Query DataSets for GSM978835
Status Public on Dec 01, 2013
Title Optimal Dose 5
Sample type RNA
Source name Tetramer-sorted M1-specific T cells, optimal dose
Organism Homo sapiens
Characteristics cell type: CD8+ T cells
treatment: influenza M1 peptide-pulsed monocyte-derived dendritic cells
peptide dosage: optimal
Treatment protocol Different peptide doses were used to pulse dendritic cells (optimal dose: 10nM; high dose: 10uM).
Growth protocol CD8+ T cells were stimulated with M1 peptide-pulsed monocyte-derived dendritic cells in complete RPMI media supplemented with T cell growth factor.
Extracted molecule total RNA
Extraction protocol T cells were harvested on D14 and tetramer sorted before Trizol-based RNA extraction.
Label Cy3
Label protocol To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer.
Hybridization protocol The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven.
Scan protocol Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies).
Description OD5
Gene expression.
Data processing The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. The signal intensities were normalized by dividing the intensity values by their median.
Submission date Jul 30, 2012
Last update date Dec 01, 2013
Contact name Yen-Ling Chiu
Organization name Johns Hopkins University
Street address 733 N. Broadway, BRB 615
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
Platform ID GPL13607
Series (1)
GSE39761 CD8+ T cell gene expression after different antigen dose stimulations

Data table header descriptions
VALUE Normalized signal intensity

Data table
4 13.999588
5 1.481023
6 11.451438
7 9.445076
8 16.889726
9 0.08264
10 1.373232
11 0.081939
12 105.458759
13 26.790067
14 7.830653
15 52.19917
16 0.080281
17 1.512499
18 0.079648
19 0.079339
20 32.134821
21 42.021824
24 4.122104
25 11.891306

Total number of rows: 58717

Table truncated, full table size 862 Kbytes.

Supplementary file Size Download File type/resource
GSM978835_OD5.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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