|
| Status |
Public on Aug 01, 2009 |
| Title |
Input-Replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
Differentiated mouse MPC-5 podocyte cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: MPC-5 podocyte cell line
fraction: input (control)
|
| Treatment protocol |
The MPC-5 cell lines were stably expressing the Wilm's Tumor protein (+KTS) isoform carrying a modified TAP tag. A fraction of each extract (Input samples) was saved and the remaining extract was applied to a sepharose IgG column, washed, and eluates were harvested after addition of TEV protease and elution in microbiospin columns.
MPC-5 cells were transferred from 33 to 37 degrees for 14 days prior to extract preparation. Four input and four eluate samples were then used to harvest RNA using Trizol.
|
| Growth protocol |
MPC-5 cells were propogated based on the recommendations in the original manuscript.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were harevsted with Trizol and qualtiy control was performed with the Agilent Bioanalyzer to confirm intact RNA prior to analysis
|
| Label |
Biotin
|
| Label protocol |
650ng of purified total RNA from four replicates each of input control extract or eluted sample were single-round amplified and biotin-labeled using the Ambion Message-Amp II-Biotin Enhanced RNA amplification kit (Applied Biosystems) according to manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
no additional information
|
| Data processing |
Raw data exported from Illumina's BeadStudio software. The normalization was simply a log2 transformation as implemented with Partek Genomics Suite v. 6.4. The log2 transformed data were then subject to further statistical analysis.
|
| |
|
| Submission date |
Jul 09, 2009 |
| Last update date |
Jul 15, 2009 |
| Contact name |
Russ P Carstens |
| E-mail(s) |
russcars@upenn.edu
|
| Phone |
215-573-1838
|
| Fax |
215-898-0189
|
| Organization name |
University Of Pennsylvania School of Medicine
|
| Department |
Medicine
|
| Street address |
411 Hill Pavilion, 380 S. University Ave.
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL6481 |
| Series (1) |
| GSE16942 |
A putative network of actin-associated cytoskeletal proteins in glomerular podocytes defined by co-purified mRNAs |
|
