|
| Status |
Public on Oct 31, 2013 |
| Title |
Cultured HSCs-LPS-1h-rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Cultured HSCs-LPS-1h-rep1
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: Primary cultured rat hepatic stellate cells
gender: Male
|
| Treatment protocol |
Cultured HSCs were treated with 10 ng / mL (final concentration) of LPS for 1h, 3h, 6h, 12h or 24h. Vehicle-treated controls were harvested at 1h or 24h.
|
| Growth protocol |
Isolated HSCs were plated at a density of 0.5 x 10^6 cells/cm^2, and the medium renewed after overnight culture and then on alternate days. The cells were used on day 7 of culture when the majority expressed α-sma but contained abundant retinoids
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cultured cells using an RNeasy Mini kit (Qiagen, Valencia, CA)
|
| Label |
biotin
|
| Label protocol |
Total RNAs were amplified and labeled using Affymetrix products [catalog #s 900371 / 900431 / 900433 / 900449] now superseded by 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA)
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2 array. GeneChips were washed and stained in an Affymetrix Fluidics Station 400.
|
| Scan protocol |
Stained microarrays were scanned with a Affymetrix GeneChip Scanner 3000
|
| Data processing |
The raw data obtained from microarray analysis were processed using Affymetrix GeneChip Operating Software (GCOS v 1.4) using software defaults, to assess the presence or absence of each transcript target sequence, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Expression levels were scaled to a target value of 500 using the software default (2% trimmed mean). Prior to scaling, global microarray signals were 279 ± 73 (mean ± SD, n = 11)
|
| |
|
| Submission date |
Aug 19, 2013 |
| Last update date |
Oct 31, 2013 |
| Contact name |
Stephen Alan Kenneth Harvey |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Pittsburgh School of Medicine
|
| Department |
Ophthalmology
|
| Lab |
EEINS 1014
|
| Street address |
203 Lothrop St
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15213-2588 |
| Country |
USA |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE49980 |
The transcriptomic response of rat hepatic stellate cells to endotoxin: implications for hepatic inflammation and immune regulation |
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