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Sample GSM1527247 Query DataSets for GSM1527247
Status Public on Apr 24, 2015
Title HSC_sample_1
Sample type RNA
 
Source name HSC cells from patient 1
Organism Homo sapiens
Characteristics cell type: Primary human hepatic stellate cells (HSCs)
Treatment protocol For stimulation of HCC cells with HSC conditioned media, HCC cells were seeded into T25 flask (10^6 cells). One day after seeding, cells were washed with serum-free DMEM, and then incubated for another 12 h with serum-free DMEM. Subsequently, the medium was changed and cells were incubated with 3 mL of HSC-CM or control medium (serum-free DMEM) for 4h.
Growth protocol The human HCC cell lines Hep3B (American Type Culture Collection (ATCC) number HB-8064) was cultured as described (Amann et al, 2009, Cancer Science). Primary human hepatic stellate cells (HSCs) were isolated from 15 different human donors as described in (Amann et al, 2009, Cancer Science). The isolation procedure and cell culture on uncoated tissue culture dishes led to the activation of HSCs. For collection of conditioned medium (CM) HSCs were seeded into T75 flasks (2 × 10^6 cells). One day after seeding cells were washed twice with serum-free DMEM, and then incubated for another 24 h with serum-free DMEM (15 mL/T75). CM was clarified by centrifugation at 6,000 g to remove cell debris, sterile filtered (0.45 μm pore size membrane filter), and stored in aliquots at −80 °C until use. Serum-free DMEM incubated for 24 h in cell culture flasks without cells served as the control.
Extracted molecule total RNA
Extraction protocol Isolation of total cellular RNA from cultured cells and tissues and reverse transcription were performed as described in Amann et al., 2009, Cancer Science.
Label biotin
Label protocol The Ambion WT Expression Kit Protocol was used for the preparation of biotinylated sense-strand cDNA from 300ng of total RNA, followed by fragmentation and labeling according to the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual.
 
Hybridization protocol 3.8 μg of fragmented and labeled sense-strand cDNA were hybridized for 16 h at 45°C on GeneChip Human Gene 1.0 ST microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Description Gene expression of hepatic stellate cells (HSC)
Data processing Raw intensity values from CEL files were normalized with the Bioconductor package VSN. Probes were summarized using median polish and an alternative CDF based on ensembl genes provided by BrainArray, University of Michigan (version 12.1.0).
 
Submission date Oct 17, 2014
Last update date Apr 25, 2015
Contact name Julia C Engelmann
E-mail(s) julia.engelmann@ur.de
Organization name University of Regensburg
Department Statistical Bioinformatics
Street address Josef-Engert-Str. 9
City Regensburg
ZIP/Postal code 93053
Country Germany
 
Platform ID GPL19306
Series (1)
GSE62455 Gene expression of paired samples of hepatic stellate cells (HSC) and hepatocyte cell culture (HCC) treated with conditioned media of HSC cells

Data table header descriptions
ID_REF
VALUE log2 expression value

Data table
ID_REF VALUE
ENSG00000000003_at 8.8473
ENSG00000000005_at 4.1318
ENSG00000000419_at 9.17
ENSG00000000457_at 6.2099
ENSG00000000460_at 5.0935
ENSG00000000938_at 5.6709
ENSG00000000971_at 8.781
ENSG00000001036_at 9.5169
ENSG00000001084_at 6.8462
ENSG00000001167_at 7.8347
ENSG00000001460_at 5.9689
ENSG00000001461_at 8.5753
ENSG00000001497_at 7.3288
ENSG00000001561_at 4.951
ENSG00000001617_at 5.9324
ENSG00000001626_at 4.2974
ENSG00000001629_at 9.0695
ENSG00000001630_at 4.0657
ENSG00000001631_at 7.2202
ENSG00000002016_at 6.4885

Total number of rows: 22197

Table truncated, full table size 561 Kbytes.




Supplementary file Size Download File type/resource
GSM1527247_A472_05_HSZ.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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