|
| Status |
Public on Jun 01, 2007 |
| Title |
autism with dup(15q) 02-07 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
pool
|
| Organism |
Homo sapiens |
| Characteristics |
Pooled total RNAs from lymphoblastoid cells of 14 individuals
|
| Growth protocol |
A total of 9x10(6) of lymphoblastoid cells were seeded in a T75 flask in 30 ml of fresh medium. Medium was RPMI1640 with 2 mM L glutamine and 25 mM HEPES and 10 percent fetal bovine serum and 1x Anitbiotic Antimicotic solution. After 24 hours total RNA was extracted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from lymphoblastoid cells of 14 individuals using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.
|
| Label |
Cy3
|
| Label protocol |
cRNA synthesis was performed using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent) according to the manufacture's protocol.
|
| |
|
| Channel 2 |
| Source name |
Autism with dup(15q) 02-07
|
| Organism |
Homo sapiens |
| Characteristics |
02-07 is a male with autism and duplication of 15q11-13.
|
| Growth protocol |
A total of 9x10(6) of lymphoblastoid cells were seeded in a T75 flask in 30 ml of fresh medium. Medium was RPMI1640 with 2 mM L glutamine and 25 mM HEPES and 10 percent fetal bovine serum and 1x Anitbiotic Antimicotic solution. After 24 hours total RNA was extracted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from lymphoblastoid cells of 02-07 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.
|
| Label |
Cy5
|
| Label protocol |
Target preparation was performed using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent) according to the manufacture's protocol.
|
| |
|
| |
| Hybridization protocol |
The generated cRNAs were mixed and subjected to hybridization to the Agilent Whole Human Genome Array G4112A according to the manufacture's protocol.
|
| Scan protocol |
Scanning of the microarray was done by Agilent DNA microarray scanner.
|
| Description |
none
|
| Data processing |
Scanner output image file was normalized and filtered using Feature Extraction Software ver 8.5. Normalization was performed so that overall intensity ratio of Cy5 to Cy3 was equal to one.
|
| |
|
| Submission date |
Mar 19, 2007 |
| Last update date |
Apr 23, 2007 |
| Contact name |
Yuhei Nishimura |
| E-mail(s) |
[email protected]
|
| Phone |
3107947537
|
| Fax |
3102672401
|
| Organization name |
University of California Los Angeles
|
| Department |
Neuropsychiatric Institute
|
| Lab |
Geschwind Lab
|
| Street address |
2309 Gonda 695 Charles E Young Dr. South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-1761 |
| Country |
USA |
| |
|
| Platform ID |
GPL1708 |
| Series (2) |
| GSE7315 |
autism with dup(15q) |
| GSE7329 |
Gene expression profiles of lymphoblastoid cells |
|
| Data table header descriptions |
| ID_REF |
identifier reference |
| VALUE |
normalized log ratio |
| CH1_SIG_MEAN |
Cy3 mean signal |
| CH2_SIG_MEAN |
Cy5 mean signal |
| CH1_BKG_MEAN |
Cy3 mean background |
| CH2_BKG_MEAN |
Cy5 mean background |
| gIsSaturated |
1 if Cy3 signal is saturated |
| rIsSaturated |
1 if Cy5 signal is saturated |
| gIsFeatNonUnifOL |
1 if Cy3 signal is nonuniform |
| rIsFeatNonUnifOL |
1 if Cy5 signal is nonuniform |
| gIsPosAndSignif |
1 if Cy3 signal is positive and significant compared with Cy3 background |
| rIsPosAndSignif |
1 if Cy5 signal is positive and significant compared with Cy5 background |
| gIsWellAboveBG |
1 if signal-to-noise ration of Cy3 is over 2.6 |
| rIsWellAboveBG |
1 if signal-to-noise ration of Cy5 is over 2.6 |
| gDyeNormSignal |
Cy3 normalized signal |
| rDyeNormSignal |
Cy5 normalized signal |
