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Sample GSM1211053 Query DataSets for GSM1211053
Status Public on Oct 31, 2013
Title Cultured HSCs-LPS-3h-rep1
Sample type RNA
Source name Cultured HSCs-LPS-3h-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Total RNAs were amplified and labeled using Affymetrix products [catalog #s 900371 / 900431 / 900433 / 900449] now superseded by 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA)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
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
VALUE GCOS 1.4 signal intensity (same algorithm at MAS 5.0)

Data table
1367452_at 6816.8
1367453_at 2968.3
1367454_at 4124.8
1367455_at 6589.6
1367456_at 10453.5
1367457_at 2386.7
1367458_at 689.7
1367459_at 12170.7
1367460_at 10246.8
1367461_at 3788.7
1367462_at 3858.8
1367463_at 3934.2
1367464_at 1235.6
1367465_at 3933
1367466_at 2649
1367467_at 2714.7
1367468_at 1405.8
1367469_at 12050.9
1367470_at 2638.6
1367471_at 1799.3

Total number of rows: 31099

Table truncated, full table size 506 Kbytes.

Supplementary file Size Download File type/resource
GSM1211053_Expt1_LPS_3h.CEL.gz 2.8 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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