|
| Status |
Public on Sep 02, 2012 |
| Title |
HEK293 control (scr for scramble) shRNA replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
human HEK293 cells infected with control (scr for scrambled) shRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
|
| Treatment protocol |
Cells were infected with lentivirus harboring control shRNA or shRNA targeting NFIL3.
|
| Growth protocol |
Human HEK293 cells were grown in DMEM supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from cells using Qiagen Rneasy kit.
|
| Label |
Cy3
|
| Label protocol |
2 µg of total RNA were labled using Agilent RNA Spike In Kit for Two color v4.0 according to manufacturer's protocol
|
| |
|
| Channel 2 |
| Source name |
Universal Human Reference RNA Stratagene
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference RNA
|
| Treatment protocol |
Cells were infected with lentivirus harboring control shRNA or shRNA targeting NFIL3.
|
| Growth protocol |
Human HEK293 cells were grown in DMEM supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from cells using Qiagen Rneasy kit.
|
| Label |
Cy5
|
| Label protocol |
2 µg of total RNA were labled using Agilent RNA Spike In Kit for Two color v4.0 according to manufacturer's protocol
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
|
| Description |
Biological replicate 2 of 6, HEK293 cells infected with scramble control shRNA (lenti-delivered pLKO.1-puro) and selected.
|
| Data processing |
Microarray data was extracted using Mean FG- Median BG (ch1=G, ch2=R), filtered: log (ch (1)*ch (2))/2>=.1, and normalized using Lowess normalization; the BASE database (Lund, Sweden) was utilized to extract, filter and normalize data.
|
| |
|
| Submission date |
Aug 16, 2011 |
| Last update date |
Sep 02, 2012 |
| Contact name |
Megan Erin Keniry |
| E-mail(s) |
mk2319@columbia.edu
|
| Phone |
212-851-5263
|
| Fax |
212-851-5267
|
| Organization name |
Columbia University
|
| Department |
Institute for Cancer Genetics
|
| Lab |
Ramon Parsons Lab
|
| Street address |
1130 St. Nicholas Ave., room 407
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL4133 |
| Series (2) |
| GSE31426 |
HEK293 cells with control or NFIL3 shRNA treatment |
| GSE31427 |
Diminishment of NFIL3 by shRNA in HEK293 and BT549 cells |
|
