|
| Status |
Public on Mar 25, 2008 |
| Title |
C2C12 Neo cell-4 RNA |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
C2C12 C3H mouse myoblast cells RNA, control (Neo)
|
| Organism |
Mus musculus |
| Characteristics |
C2C12 C3H mouse myoblast cells RNA, control (Neo)
|
| Biomaterial provider |
ATTC-Yao Lab
|
| Growth protocol |
Sample is C2C12 cells stably selected with a Neo encoding retrovirus that were grown to 90% confluence and starved with 2% horse serum for 4 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was accomplished by extracting RNA using TriReagent (Molecular Research Center, Inc.). The RNA (10 µg) was DNase treated using a DNA-free kit (Ambion) and assessed for quality with an Agilent Lab-on-a-Chip 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).
|
| Label |
Cy5
|
| Label protocol |
The RNA from cells was directly labeled with Cy dyes using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labeling and hybridization protocols.
|
| |
|
| Channel 2 |
| Source name |
Murine Reference RNA
|
| Organism |
Mus musculus |
| Characteristics |
Murine Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of murine genes was used.
|
| Biomaterial provider |
Stratagene
|
| Extracted molecule |
total RNA |
| Extraction protocol |
None
|
| Label |
Cy3
|
| Label protocol |
The RNA from murine liver was directly labeled with Cy dyes using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labeling and hybridization protocols.
|
| |
|
| |
| Hybridization protocol |
Hybridization of a Cy labeled cDNA probe (mix of Cy3 and Cy5) onto coated slide spotted with oligonucleotides (70mers) was performed as described in detail at http://mgm.duke.edu/genome/dna_micro/core/protocols/SOP_hyb.doc.
|
| Scan protocol |
Fluorescent array images were collected for both Cy3 and Cy5 with a Axon GenePix Pro 4000A scanner and image intensity data were extracted and analyzed with Microarray Analysis Suite (MAS) 5.0 software.
|
| Description |
All microarray procedures performed by Duke University Microarray Core Facility.
|
| Data processing |
VALUE column is the log2 ratio of normalized Cy5:Cy3 signal after Intensity-Dependent normalization.
|
| |
|
| Submission date |
Feb 21, 2008 |
| Last update date |
Feb 29, 2008 |
| Contact name |
Zachary Conrad Hartman |
| E-mail(s) |
zch@duke.edu
|
| Phone |
919-684-9197
|
| Organization name |
Duke University
|
| Department |
Surgery
|
| Lab |
Lyerly Lab
|
| Street address |
Research Drive MSRB rm 414
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL3222 |
| Series (1) |
| GSE10678 |
Histone deacetylase 4 represses dystrophin-glycoprotein (DGC) complex expression |
|
