NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1501645 Query DataSets for GSM1501645
Status Public on Nov 12, 2014
Title HepG2
Sample type RNA
 
Source name HepG2, passage15
Organism Homo sapiens
Characteristics cell type: HepG2, passage15
Treatment protocol For each human iPSC line for hepatocyte differentiation, all differentiated cells are constantly removed by manually picking up. Before the initiation of hepatocyte differentiation, human iPSCs were dissociated into clumps by using dispase (Roche) and plated onto BD Matrigel Basement Membrane Matrix Growth Factor Reduced (BD Biosciences). These cells were cultured in the MEF-conditioned medium for 3-4 days. The differentiation protocol for the induction of definitive endoderm cells, hepatoblasts, and hepatocytes was based on our previous reports with some modifications. Briefly, in the definitive endoderm differentiation, human iPSCs were cultured for 4 days in the L-Wnt3A-expressing cell (ATCC, CRL2647)-conditioned RPMI1640 medium (Sigma) which contains 100 ng/ml Activin A (R&D Systems), 4 mM L-Glutamine, 0.2% FBS (PAA Laboratories), and 1×B27 Supplement Minus Vitamin A (Life Technologies). For the induction of HBCs, the definitive endoderm cells were cultured for 5 days in RPMI1640 medium (Sigma) which contains 30 ng/ml bone morphogenetic protein 4 (BMP4) (R&D Systems) and 20 ng/ml FGF4 (R&D Systems), 4 mM L-Glutamine, and 1×B27 Supplement Minus Vitamin A. The protocol for HBC proliferation using human recombinant laminin-111 (BioLamina) was based on our previous report with some modifications. Briefly, the hPSC-derived HBCs were first purified from the hPSC-derived cells (day 9) by selecting attached cells on a human recombinant LN111-coated dish (final coating concentration was 1.0 μg/cm2) at 15 min after plating. The hPSC-derived HBCs were cultured on a human LN111-coated dish (2.5 × 104 cells/cm2) in maintenance DMEM/F12 medium (DMEM/F12 medium (Invitrogen) was supplemented with 10% FBS (PAA laboratories), 1×insulin/transferrin/selenium, 10 mM nicotinamide, 10-7 M Dexamethasone (DEX) (Sigma), 20 mM HEPES, 25 mM NaHCO3, 1×GlutaMAX, 40 ng/ml hepatocyte growth factor (HGF) (R&D Systems) and 20 ng/ml epidermal growth factors (EGF) (R&D Systems)). The medium was refreshed every day. The HBCs were dissociated with Accutase (Millipore) into single cells, and subcultured every 6 or 7 days. To perform the hepatocyte differentiation, the HBCs were cultured for 5 days in RPMI1640 medium (Sigma) which contains 20 ng/ml HGF, 4 mM L-Glutamine, and 1×B27 Supplement Minus Vitamin A. And then, the cells were cultured for 11 days in Hepatocyte Culture Medium (HCM, Lonza) without EGF but with 20 ng/ml oncostatin M (OsM). Unlike our previous reports, the current differentiation method could omit the use of adenovirus-mediated overexpression of hepatic transcription factors.
Extracted molecule total RNA
Extraction protocol RNA was extracted using RNeasy Mini Kit.
Label Cy3
Label protocol 100 ng total RNA from all samples was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.
 
Hybridization protocol Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (8x60K v2, Design ID 039494) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.
Scan protocol Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).
Description HepG2
Data processing The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.
 
Submission date Sep 10, 2014
Last update date Apr 23, 2018
Contact name Kazuo Takayama
E-mail(s) [email protected]
Phone +81-75-366-7362
Organization name Kyoto University
Department Center for iPS Cell Research and Application
Street address Shogoin Kawaharacho 53, Sakyo-ku
City Kyoto
State/province Kyoto
ZIP/Postal code 6068507
Country Japan
 
Platform ID GPL16699
Series (1)
GSE61287 Gene expression profiles in PHH-iPSCs, PHH-HLCs, PHHs, and HepG2
Relations
Reanalyzed by GSE113533

Data table header descriptions
ID_REF
VALUE median normalized signal intensities (without controls)
gIsPosAndSignif

Data table
ID_REF VALUE gIsPosAndSignif
4 332.26121 1
5 0.303856 0
6 0.305569 0
7 0.772961 1
8 0.830521 1
9 20929.94265 1
10 23.257181 1
11 0.311721 0
12 1140.264548 1
13 8.65422 1
14 0.314009 0
15 0.314581 0
16 0.315073 0
17 711.16551 1
18 22.193753 1
19 0.315939 0
20 605.562796 1
21 0.316092 0
22 0.316059 0
23 0.315966 0

Total number of rows: 58717

Table truncated, full table size 988 Kbytes.




Supplementary file Size Download File type/resource
GSM1501645_253949415026_S01_GE1_107_Sep09_1_2.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap