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Sample GSM1520966 Query DataSets for GSM1520966
Status Public on Apr 15, 2015
Title Mouse cochlea of 4 weeks of age #2
Sample type RNA
 
Source name Mouse cochlea of 4 weeks of age
Organism Mus musculus
Characteristics age: 4 weeks of age
Sex: male
tissue: cochlea
strain: DBA/2J
Treatment protocol DBA/2J mice (4 weeks old) were injected subcutaneously once daily for 8 weeks with L-methionine (500 mg/kg) and valproic acid (300 mg/kg) in 0.1M sodium bicarbonate.
Growth protocol Mice were housed in plastic cages with metallic lid in a room with a 12-h light/dark cycle and 55% humidity at 23 C and had free access to food and water.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from mouse whole cochlea using TRIzol regent (LifeTechnologies). Additionally, total RNA was purified using Rneasy Mini Kit (Qiagen).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Rev. 3, 2009, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix Scanner 3000 7G.
Data processing The data were digitalized using GeneChip Operating Software (GCOS) v.1.3 (Affymetrix).
Gene expression array data were normalized using MAS5 algorithm (Affymetrix). Then, to correct for bias between chips, quantile normalization (Bolstad, B. M. et al. Bioinformatics 19, 185-193 (2003)) was applied to all array data using R software.
The intensities were converted to a logarithmic scale (base 2). Signal reliability of each probe was determined based on the MAS5 Call algorithm (Affymetrix), and each probe was assigned to one of three flags (P: present, M: marginal, and A: absent).
 
Submission date Oct 08, 2014
Last update date Apr 15, 2015
Contact name Fuyuki Miya
E-mail(s) fmiya@keio.jp
Phone +81-3-5363-3890
Organization name Keio University
Department School of Medicine
Lab Center for Medical Genetics
Street address 35 Shinanomachi, Shinjuku-ku
City Tokyo
State/province Tokyo
ZIP/Postal code 160-8582
Country Japan
 
Platform ID GPL1261
Series (1)
GSE62173 Expression data of mice cochlea treated with L-methionine and valproic acid.

Data table header descriptions
ID_REF
VALUE log2 processed signal intensity
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
1415670_at 10.43195778 P
1415671_at 11.86555236 P
1415672_at 12.82705922 P
1415673_at 9.656032098 P
1415674_a_at 10.98364178 P
1415675_at 10.47127602 P
1415676_a_at 11.99957089 P
1415677_at 9.603283925 P
1415678_at 11.60947078 P
1415679_at 12.14334493 P
1415680_at 9.182111474 P
1415681_at 10.98438265 P
1415682_at 10.80988266 P
1415683_at 11.97306678 P
1415684_at 9.982546463 P
1415685_at 9.567071411 P
1415686_at 11.45657612 P
1415687_a_at 12.70814094 P
1415688_at 11.83158947 P
1415689_s_at 10.7433722 P

Total number of rows: 45101

Table truncated, full table size 1114 Kbytes.




Supplementary file Size Download File type/resource
GSM1520966_Untreated_4-weeks_2.CEL.gz 6.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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