|
| Status |
Public on Dec 02, 2013 |
| Title |
GM09582 Mock vs. GM09582 1.5 Gy Gamma |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
GM09582 Mock
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GM09582 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research
treatment: 0 Gy IR + 6 hr
disease state: Ataxia telangiectasia affected individual
age: 12 yr old
ethnicity: caucasian
gender: female
|
| Biomaterial provider |
GM09582 lymphoblast cells from Coriell Institute for Medical Research
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM09582
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy technology following the manufacturer's instructions with the RNeasy Midi Kit
|
| Label |
Cy3
|
| Label protocol |
Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.
|
| |
|
| Channel 2 |
| Source name |
GM09582 1.5 Gy Gamma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GM09582 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research
treatment: 1.5 Gy IR + 6 hr
disease state: Ataxia telangiectasia affected individual
age: 12 yr old
ethnicity: caucasian
gender: female
|
| Biomaterial provider |
GM09582 lymphoblast cells from Coriell Institute for Medical Research
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM09582
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy technology following the manufacturer's instructions with the RNeasy Midi Kit
|
| Label |
Cy5
|
| Label protocol |
Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500ng of total RNA, Cy5 labeled cRNA was produced according to manufacturer’s protocol.
|
| |
|
| |
| Hybridization protocol |
For each two color comparison, equal amounts of Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.
|
| Scan protocol |
Slides were washed as indicated in the Agilent 60-mer oligo microarray processing protocol and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters.
|
| Description |
Cultures were maintained in RPMI 1640 media supplemented with 15% fetal bovine serum and L-glutamine. Cells were plated in T25 flasks and cultured for 2 days prior to exposure to gamma radiation. Cells were harvested 6 hours after mock irradiation or irradiation with 1.5 Gy gamma radiation. Harvesting cells consisted of spinning the cells and media and aspirating the supernatant. Pellets were flash frozen in liquid nitrogen and stored at -80oC.
|
| Data processing |
Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters and loaded into the Rosetta Resolver® system (v6.0) (Rosetta Biosoftware, Kirkland, WA).
|
| |
|
| Submission date |
Dec 02, 2009 |
| Last update date |
Dec 02, 2013 |
| Contact name |
NIEHS Microarray Core |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
NIEHS
|
| Department |
DIR
|
| Lab |
Microarray Core
|
| Street address |
111 T.W. Alexander Drive
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL7260 |
| Series (1) |
| GSE19287 |
ATM-dependent Transcriptional Responses to 1.5 Gy Gamma Radiation in Human Lymphocytes |
|
