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Status |
Public on Aug 01, 2009 |
Title |
Eluate-Replicate 2 |
Sample type |
RNA |
|
|
Source name |
Differentiated mouse MPC-5 podocyte cell line
|
Organism |
Mus musculus |
Characteristics |
cell line: MPC-5 podocyte cell line fraction: eluate
|
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.
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|
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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.
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|
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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 |
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