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Sample GSM2440843 Query DataSets for GSM2440843
Status Public on Jan 16, 2017
Title WT(cy3) vs KO(cy5) biological replicate 1
Sample type RNA
 
Channel 1
Source name Lamtor1-deficient CD4+ T cells
Organism Mus musculus
Characteristics strain: C57BL/6J
genotype/variation: KO
Treatment protocol CD4+CD62L+ naïve T cells were were cultured in RPMI medium and stimulated with anti-CD28 mAb and, plate-coated anti-CD3 mAb described previously for 5 days in the addition of 50 ng/ml IL-2, and 1 ng/ml rhTGFβ.
Growth protocol CD4+CD62L+ naïve T cells were purified from spleens using an automated magnetic cell sorter.
Extracted molecule total RNA
Extraction protocol Total RNA of the CD4+CD62L+ naïve T was extracted RNeasy mini kit (Qiagen) according to the manjufacturer’s instructions.
Label Cy5
Label protocol Differentially labeled 400 ng of each cRNA samples were hybridized on microarray slides. Samples were then hybridized on Agilent 4 × 44K ver.2 whole mouse genome arrays (Agilent Design # 026655) at 65 °C for 17 h with rotation in the dark. Hybridization was performed using the Gene Expression Hybridization Kit (Agilent Technologies Inc., Santa Clara, CA, USA) following the manufacturer's instructions.
 
Channel 2
Source name WT CD4+ T cells
Organism Mus musculus
Characteristics genotype/variation: WT
Treatment protocol CD4+CD62L+ naïve T cells were were cultured in RPMI medium and stimulated with anti-CD28 mAb and, plate-coated anti-CD3 mAb described previously for 5 days in the addition of 50 ng/ml IL-2, and 1 ng/ml rhTGFβ.
Growth protocol CD4+CD62L+ naïve T cells were purified from spleens using an automated magnetic cell sorter.
Extracted molecule total RNA
Extraction protocol Total RNA of the CD4+CD62L+ naïve T was extracted RNeasy mini kit (Qiagen) according to the manjufacturer’s instructions.
Label Cy3
Label protocol Differentially labeled 400 ng of each cRNA samples were hybridized on microarray slides. Samples were then hybridized on Agilent 4 × 44K ver.2 whole mouse genome arrays (Agilent Design # 026655) at 65 °C for 17 h with rotation in the dark. Hybridization was performed using the Gene Expression Hybridization Kit (Agilent Technologies Inc., Santa Clara, CA, USA) following the manufacturer's instructions.
 
 
Hybridization protocol After washing in GE washing buffer, the slide was scanned with Agilent Microarray Scanner G2505C.
Scan protocol Images were quantified using Agilent Feature Extraction Software (version.10.5.1.1).
Description WT(cy3) vs KO(cy5) biological replicate 1
Data processing Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.
 
Submission date Dec 27, 2016
Last update date Jan 16, 2017
Contact name Daisuke Okuzaki
E-mail(s) dokuzaki@biken.osaka-u.ac.jp
Phone +81-6-6879-4935
Organization name Osaka univ.
Department Immunology Frontier Research Center
Lab Human Immunology (Single Cell Genomics)
Street address Yamadaoka 3-1
City Suita
State/province Osaka
ZIP/Postal code 565-0871
Country Japan
 
Platform ID GPL10333
Series (1)
GSE92946 Essential roles of Lamtor1 in CD4+ T cell-mediated autoimmunity

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 1.217312819e-001
2 0.000000000e+000
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 0.000000000e+000
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 0.000000000e+000
12 -2.945879120e-001
13 0.000000000e+000
14 3.540623749e-001
15 7.916291470e-001
16 -4.285754334e-003
17 -1.866335115e-001
18 0.000000000e+000
19 0.000000000e+000
20 0.000000000e+000

Total number of rows: 44397

Table truncated, full table size 1003 Kbytes.




Supplementary file Size Download File type/resource
GSM2440843_1_cy3-WT_vs_cy5-KO_1_1.txt.gz 15.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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