|
| Status |
Public on Dec 31, 2013 |
| Title |
fos_GPE_day7_rep1 [Cy3/Cy5] |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
RNA from cells over-expressing factor
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J
protocol: transfected with fos
time point: day7
cell type: GPE
|
| Treatment protocol |
10 µg of total RNA was isolated from Trizol (Invitrogen, Burlington, ON, Canada) samples of either NIH 3T3 cells or GP+E86 cells 3-7 days after transfection with either empty vector or vectors overexpressing individual factors.
|
| Growth protocol |
cells were tranduced with lentiviral expression vector containing cDNA for test protein and grown for 3 or 7 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Channel 2 |
| Source name |
RNA from cells with empty vector
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J
time point: day7
cell type: GPE
protocol: transduced with empty vector (control)
|
| Treatment protocol |
10 µg of total RNA was isolated from Trizol (Invitrogen, Burlington, ON, Canada) samples of either NIH 3T3 cells or GP+E86 cells 3-7 days after transfection with either empty vector or vectors overexpressing individual factors.
|
| Growth protocol |
cells were tranduced with lentiviral expression vector containing cDNA for test protein and grown for 3 or 7 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).
|
| Label |
Cy5
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol except that 3ug of each of the test and control samples were hybed, rather than 6ug of the test. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed on an Axon 4000b scanner in two channels as per the guidelines by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of fos
|
| Data processing |
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 data extraction. Values for each channel were divided to compute a ratio (overexpressed factor vs. control).
|
| |
|
| Submission date |
Aug 02, 2012 |
| Last update date |
Dec 31, 2013 |
| Contact name |
Brian Wilhelm |
| E-mail(s) |
brian.wilhelm@umontreal.ca
|
| Organization name |
University of Montreal
|
| Street address |
2950 Chemin Polytechnique
|
| City |
Montreal |
| ZIP/Postal code |
H1J 3R4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL15882 |
| Series (1) |
| GSE39835 |
A Novel Osteoclastic Network Determines Niche for Mouse Hematopoietic Stem Cells In Vitro |
|
