|
| Status |
Public on Mar 05, 2012 |
| Title |
R1 shCdk8-1 replicate 1 - 13 days |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
R1 mouse ES cells + shCdk8-1, 13 days
|
| Organism |
Mus musculus |
| Characteristics |
cell line: R1
knockdown: shCdk8-1
time: 13 days
|
| Treatment protocol |
R1 cells were infected with shNTC, shCdk8-1, shCdk8-2, shMed12-1, or shMed12-2 using lentivirus.
|
| Growth protocol |
R1 cells were grown for 8 days or 13 days after shRNA infection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Qiagen RNeasy kit following manufacturer's protocol, including on-column DNase-digestion. RNA was quantified using UV-spec Nanodrop and then profiled on Agilent Bioanalyzer.
|
| Label |
Cy5
|
| Label protocol |
Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Low RNA Input Fluorescent Linear Amplification Kit. 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).
|
| |
|
| Channel 2 |
| Source name |
Stratagene universal mouse reference RNA
|
| Organism |
Mus musculus |
| Characteristics |
sample type: Stratagene universal mouse reference RNA
cell line: Mixture of multiple mouse cell lines
|
| Treatment protocol |
R1 cells were infected with shNTC, shCdk8-1, shCdk8-2, shMed12-1, or shMed12-2 using lentivirus.
|
| Growth protocol |
R1 cells were grown for 8 days or 13 days after shRNA infection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Qiagen RNeasy kit following manufacturer's protocol, including on-column DNase-digestion. RNA was quantified using UV-spec Nanodrop and then profiled on Agilent Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Low RNA Input Fluorescent Linear Amplification Kit. 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).
|
| |
|
| |
| Hybridization protocol |
Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried, and then scanned.
|
| Scan protocol |
Scanned on an Agilent scanner; images were processed using Agilent Feature Extraction software version 10.7.
|
| Description |
Biological replicate 1 of 3. shCdk8-1 treated for 13 days
|
| Data processing |
Agilent Feature Extraction software version 10.7 was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Jul 20, 2011 |
| Last update date |
Mar 05, 2012 |
| Contact name |
Adam S Adler |
| E-mail(s) |
a.adler55@gmail.com
|
| Organization name |
Genentech
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL7202 |
| Series (2) |
| GSE30816 |
CDK8 and MED12 knockdown in R1 mouse ES cells |
| GSE30817 |
CDK8 knockdown in HT-29 cells and CDK8 & MED12 knockdown in R1 cells |
|
