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Sample GSM1607135 Query DataSets for GSM1607135
Status Public on Mar 03, 2015
Title S23265 -T cell lymphoma compared to sex-matched ear DNA reference
Sample type genomic
 
Channel 1
Source name S23265-T cell lymphoma
Organism Mus musculus
Characteristics Sex: Female
dose group: Carbon-1 x 4 Gy
Treatment protocol Ear tissue or T cell lymphoma cell suspensions stored frozen at -80°C since autopsy were used to extract genomic DNA
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from T cell lymphoma cells or sex-matched mouse ear tissue using an automated Maxwell-16 DNA Purification kit, then 2-3 μg of DNA was further purified by RNase treatment followed by phenol/chloroform re-extraction
Label Cy5
Label protocol 250 ng of purified DNA was digested with Alu I and Rsa I restriction enzymes for 2 h at 37°C, then fluorescently labelled with Cy3/Cy5 using the Agilent SureTag Complete DNA labelling kit using the 'half-volume' protocol for use with 8-pack array slides
 
Channel 2
Source name S23265 Ear
Organism Mus musculus
Characteristics Sex: Female
dose group: Carbon-1 x 4 Gy
Treatment protocol Ear tissue or T cell lymphoma cell suspensions stored frozen at -80°C since autopsy were used to extract genomic DNA
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from T cell lymphoma cells or sex-matched mouse ear tissue using an automated Maxwell-16 DNA Purification kit, then 2-3 μg of DNA was further purified by RNase treatment followed by phenol/chloroform re-extraction
Label Cy3
Label protocol 250 ng of purified DNA was digested with Alu I and Rsa I restriction enzymes for 2 h at 37°C, then fluorescently labelled with Cy3/Cy5 using the Agilent SureTag Complete DNA labelling kit using the 'half-volume' protocol for use with 8-pack array slides
 
 
Hybridization protocol Labelled DNA was hybridised in 1X Agilent Blocking Agent/Hi-RPM Buffer at 65°C for 24 h in a rotating hybridisation oven, then the slides were washed in Oligo aCGH Wash Buffer 1 and 2
Scan protocol The slides were scanned in an Agilent DNA Microarray scanner (G2565CA)
Data processing Agilent Feature Extraction Software (10.7.3.1) was used for computing ratios
Normalised log2 ratio [T-cell lymphoma (test)/Ear (reference)] either Cy3/Cy5 or Cy5/Cy3 depending on the array slide
 
Submission date Feb 10, 2015
Last update date Mar 03, 2015
Contact name Benjamin John Blyth
E-mail(s) benjamin.blyth@gmail.com
Organization name National Institute of Radiological Sciences
Department Centre for Radiation Protection
Lab Radiation for Children's Health Program
Street address 4-9-1 Anagawa
City Inage-ku
State/province Chiba
ZIP/Postal code 2638555
Country Japan
 
Platform ID GPL19767
Series (1)
GSE61315 Radiation-Induced T Cell Lymphoma: Carbon ion- vs. Gamma Ray-Induced

Data table header descriptions
ID_REF
VALUE Normalised log2 ratio T-cell lymphoma (test)/Ear (reference)

Data table
ID_REF VALUE
A_67_P04000012 0.3557468
A_67_P04000058 0.35656932
A_67_P00000082 0.3383406
A_67_P00000133 0.4932553
A_67_P00000185 0.24675593
A_67_P04000400 0.41603303
A_67_P04000501 0.35431668
A_67_P04000664 0.670317
A_67_P04000834 0.30804533
A_67_P00000662 0.36185363
A_67_P04001017 0.48701778
A_67_P04001131 0.44220832
A_67_P04001245 0.45249763
A_67_P04001347 0.4189947
A_67_P04001449 0.64681166
A_67_P04001560 0.3940802
A_67_P00001198 0.59255546
A_67_P00001289 0.49609724
A_67_P00001369 0.33240494
A_67_P00001423 0.55586004

Total number of rows: 52500

Table truncated, full table size 1291 Kbytes.




Supplementary file Size Download File type/resource
GSM1607135_S23265.txt.gz 6.5 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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