|
| Status |
Public on Oct 01, 2008 |
| Title |
stable control replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Stratagene Universal Reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
Pooled cell line RNA
|
| Treatment protocol |
BJAB and BCBL-1 cells were electroporated with siPORT system (Ambion) at 30 nM for mimics and 100 nM for inhibitors (RNA harvested 48 and 72 hr. after transfection, respectively)
|
| Growth protocol |
Cells were split to 2x10^5 cells per ml every 48 hr.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested with RNA-bee (Tel-test). RNA integrity was assayed using a Bioanalyzer 2100 (Agilent) and quantitated with a ND1000 spectrophotometer (Nanodrop).
|
| Label |
cy3
|
| Label protocol |
500 ng of total RNA was labeled using Low RNA Input Fluor Linear Amp Kit PLUS (Agilent).
|
| |
|
| Channel 2 |
| Source name |
stable BJAB cell line
|
| Organism |
Homo sapiens |
| Characteristics |
transduced with retrovirus
|
| Treatment protocol |
BJAB and BCBL-1 cells were electroporated with siPORT system (Ambion) at 30 nM for mimics and 100 nM for inhibitors (RNA harvested 48 and 72 hr. after transfection, respectively)
|
| Growth protocol |
Cells were split to 2x10^5 cells per ml every 48 hr.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested with RNA-bee (Tel-test). RNA integrity was assayed using a Bioanalyzer 2100 (Agilent) and quantitated with a ND1000 spectrophotometer (Nanodrop).
|
| Label |
cy5
|
| Label protocol |
500 ng of total RNA was labeled using Low RNA Input Fluor Linear Amp Kit PLUS (Agilent).
|
| |
|
| |
| Hybridization protocol |
Samples were prepared with Gene Expression Hybridization Kit (Agilent) and placed in Agilent microarray hybridization chambers and rack. Hybridization occurred for 17 hr. at 65°.
|
| Scan protocol |
Scanned on Axon Genepix 4000B scanner. Images were processed with Agilent Feature Extraction Software v9.1.1.
|
| Description |
stable BJAB control cell line. Biological replicate 1 of 2.
|
| Data processing |
Linear LOWESS normalization was used. Default Agilent normalization was employed within Genespring GX. In detail, Each gene's measured intensity was divided by its control channel value in each sample; if the control channel was below 0 then 0 was used instead. If the control channel and the signal channel were both below 0 then no data was reported. Each measurement was divided by the 50.0th percentile of all measurements in that sample. The percentile was calculated using only genes marked present. Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 0 then each measurement for that gene was divided by 0 if the numerator was above 0, otherwise the measurement was thrown out.
|
| |
|
| Submission date |
Sep 29, 2008 |
| Last update date |
Sep 30, 2008 |
| Contact name |
Don Ganem |
| E-mail(s) |
ganem@cgl.ucsf.edu
|
| Phone |
(415) 476 - 2826
|
| Organization name |
University of California, San Francisco
|
| Department |
G.W. Hooper
|
| Street address |
513 Parnassus Ave
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143-0552 |
| Country |
USA |
| |
|
| Platform ID |
GPL6848 |
| Series (1) |
| GSE12967 |
miR-K5 expression and inhibition |
|
