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Sample GSM575142 Query DataSets for GSM575142
Status Public on Feb 17, 2011
Title CskKO/Src_biological rep1
Sample type RNA
 
Source name Csk-/- C57BL/6J MEFs expressing c-Src
Organism Mus musculus
Characteristics strain: C57BL/6J
genotype: Csk-/-
cell type: mouse embryonic fibroblasts (MEFs)
transfection: Src
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Sepazol (Nacalai Tesque, Kyoto, Japan) according to the manufacturer’s instructions. RNA yield and A260/280 ratio were monitored with a NanoDropND-100 spectrometer (Thermo Scientific, Wilmington, DE), and RNA integrity numbers were assessed with the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Only RNA extracts with RNA integrity number values >9 were included in further analyses.
Label Cy3
Label protocol One hundred nanograms of aliquots of total RNA was used for making miRNA probes according to the Agilent protocol (ver. 1.6). Briefly, total RNA was dephosphorylated with calf intestine alkaline phosphatase (Takara Bio, Shiga, Japan), denatured with dimethyl sulfoxide, and labeled with pCp-Cy3 using T4 RNA ligase (Takara Bio, Shiga, Japan) using the miRNA Labeling Reagent and Hybridization Kit (5190-0408, Agilent).
 
Hybridization protocol Refer to Agilent miRNA hybridisation protocol. Probes were hybridized at 55°C for 20 hours with rotation. Then the slides were washed by Gene expression wash buffer 1 at room temperature for 5 minutes and by Gene expression wash buffer 2 at 37°C for 5 minutes.
Scan protocol After hybridization and washing, the slides were scanned using an Agilent scanner (G2505B). Images were extracted using Agilent Feature Extraction software (ver. 9.5.3.1) and Agilent GeneSpring GX software (ver. 10.0.2).
Description CskKO/Src-rep1
Csk-/- mouse embryonic fibroblasts (Csk-/- MEFs) expressing c-Src.
Data processing Data were processed by the Agilent GeneSpring GX software. Total gene signal from GeneView data files extracted with default settings in Agilent Feature Extraction, which summarized the measurements of all probes for each gene on an array, was used as signal for miRNAs. To avoid missing values after log-transformation, any signal which was still less than 1 was reset to be equal to 1. Differences in miRNA expressions between the 4 pairs was determinate if the fold change of expression values was >2.0 and the p value was <0.05 using Student's t test for further analysis.
 
Submission date Aug 04, 2010
Last update date Feb 18, 2011
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 GPL9756
Series (1)
GSE23426 Analysis of the miRNA profile associated with c-Src-mediated transformation

Data table header descriptions
ID_REF
VALUE Normalized Cy3 signal intensity (=gTotalGeneSignal)

Data table
ID_REF VALUE
miRNABrightCorner30 839.97797
DarkCorner 3.90201
mmu-miR-384-5p 1
mmu-miR-32 15.199402
mmu-miR-466a-5p 1
mmu-miR-155 132.378
mmu-let-7f 2918.16
mmu-miR-669k 1
mmu-miR-488* 1
mmu-miR-297a* 4.04558
mmu-miR-503* 1
mmu-miR-1897-5p 38.11931
mmu-miR-374* 1
mmu-miR-669h-5p 1
mmu-miR-30e 395.99103
mmu-miR-369-3p 1
mmu-miR-1186 1
mmu-miR-699 1.37015
mcmv-miR-m21-1 1
mmu-miR-190 2.70104

Total number of rows: 672

Table truncated, full table size 12 Kbytes.




Supplementary file Size Download File type/resource
GSM575142.txt.gz 1.7 Mb (ftp)(http) TXT
GSM575142_GeneView.txt.gz 7.7 Kb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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