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Sample GSM1211059 Query DataSets for GSM1211059
Status Public on Oct 31, 2013
Title Cultured HSCs-LPS-1h-rep2
Sample type RNA
 
Source name Cultured HSCs-LPS-1h-rep2
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Total RNAs were amplified and labeled using Affymetrix products [catalog #s 900371 / 900431 / 900433 / 900449] now superseded by 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA)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) stephenaharvey@cs.com
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

Data table header descriptions
ID_REF
VALUE GCOS 1.4 signal intensity (same algorithm at MAS 5.0)

Data table
ID_REF VALUE
1367452_at 6814.2
1367453_at 2292.7
1367454_at 2790
1367455_at 4484.6
1367456_at 8873.6
1367457_at 3008.5
1367458_at 769.4
1367459_at 11357.9
1367460_at 9058.3
1367461_at 3332.8
1367462_at 2859.8
1367463_at 3859.3
1367464_at 920.5
1367465_at 2596.3
1367466_at 1717.3
1367467_at 3601.5
1367468_at 1347.3
1367469_at 8661.6
1367470_at 2870.8
1367471_at 1670.9

Total number of rows: 31099

Table truncated, full table size 507 Kbytes.




Supplementary file Size Download File type/resource
GSM1211059_Expt2_LPS_1h.CEL.gz 2.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table
Processed data are available on Series record

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