|
| Status |
Public on Apr 30, 2014 |
| Title |
myr-SetB_2, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
myr-SetB-transfected RGCs
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
age: postnatal day 4 (P4)
cell type: purified retinal ganglion cells (RGC)
transfected with: myr-Set-β (w/ pMAX-GFP)
cell subtype: FACS-isolated, GFP positive RGCs
|
| Treatment protocol |
Postnatal rat retinal ganglion cells (RGC) were electroporated with constructs immediately after isolation by immunopanning and then plated in glass bottom dishes uncoated with any substrate. Transfected RGCs were FACS-isolated next day and cultured two more days on laminin prior to isolation of RNA.
|
| Growth protocol |
Postnatal rat retinal ganglion cells were purified by immunopanning and cultured in defined growth medium “full-sato” prior to isolation of RNA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The Quick-RNA MicroPrep kit (R1050, Zymo Research) was used for RNA extraction according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
5 µg of cDNA product from each sample was used as input for fragmentation and labeling using the Encore Biotin Module kit (4200-12, NuGEN).
|
| |
|
| Hybridization protocol |
The labeled product was hybridized to whole genome GeneChip Rat Gene 2.0 ST Arrays (Affymetrix).
|
| Scan protocol |
The staining, washing and scanning of the arrays was carried out using a Fluidics 450 station, GeneChip Operating Software and GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
Transfected cells FACS-isolated
|
| Data processing |
Image intensities were analyzed with Expression Console (Affymetrix) from CEL files for quality control using standard GeneChip Rat Gene 2.0 ST Array control probes (Affymetrix), and to determine the RMA expression signal intensity values and for annotations.
|
| |
|
| Submission date |
Apr 21, 2014 |
| Last update date |
Apr 30, 2014 |
| Contact name |
Ephraim F Trakhtenberg |
| E-mail(s) |
trakhtenberg@uchc.edu
|
| Organization name |
University of Connecticut School of Medicine
|
| Department |
Neuroscience
|
| Street address |
263 Farmington Ave. RM L4005
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06030 |
| Country |
USA |
| |
|
| Platform ID |
GPL17117 |
| Series (1) |
| GSE56951 |
Regulation of gene expression by Set-beta in rat retinal ganglion cells |
|
