|
| Status |
Public on Mar 03, 2015 |
| Title |
S22570 -T cell lymphoma compared to sex-matched ear DNA reference |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
S22570-T cell lymphoma
|
| Organism |
Mus musculus |
| Characteristics |
Sex: Female
dose group: Carbon-4 x 1 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
|
| |
|
| Channel 2 |
| Source name |
S22708 Ear
|
| Organism |
Mus musculus |
| Characteristics |
Sex: Female
dose group: Carbon-4 x 1 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
|
| |
|
| |
| 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 |
|
