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Sample GSM1372817 Query DataSets for GSM1372817
Status Public on Apr 30, 2014
Title IHCC_IDH2_WT_Collagen_Rep2
Sample type RNA
 
Source name HBs_wild type IDH2_collagen-coated plates
Organism Mus musculus
Characteristics cell type: hepatoblasts (HBs) from E14 WT mouse
genotype/variation: expressing wild type IDH2
culture plate: collagen-coated plate
Treatment protocol For IDH1 experiments, culture media was supplemented with 25 ng/mL of doxycycline (d9891, Sigma-Aldrich). For hepatocyte differentiation assays, 5e6 HB cells were cultured on uncoated 10 cm tissue culture dishes in HB cell medium for up to 5 days and isolated for gene expression analysis.
Growth protocol HB cells were prepared from WT mice at embryonic day 14 and immortalized by plating at clonal density. HBs were maintained in HB media [DMEM/F-12 (Gibco Life Technologies, Grand Island NY) containing 10% fetal bovine serum, 1% penicillin-streptomycin, 50ng/mL epidermal growth factor, 30 ng/mL insulin-like growth factor II (PeproTech, Rocky Hill, NJ), 10 μg/mL insulin (Roche, Mannheim, Germany)] on plates coated with rat tail collagen (BD Biosciences, Bedford, MA) in a humidified atmosphere with 5% CO2 at 37°C.
Extracted molecule total RNA
Extraction protocol Total RNA (1ug) was isolated using RNeasy Mini Kit (QIAGEN, Valencia, CA) and quality control performed using Bioanalyzer 2100 (Agilent Technologies).
Label biotin
Label protocol First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
 
Hybridization protocol The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to Affymetrix 430Av2 microarray chips overnight at 45°C. The hybridization solution is then removed. The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe.
Scan protocol Scans were performed on Affymetrix confocal laser scanners.
Description Cholangio_IDH2_WT_Collagen_2
Data processing Raw expression values were normalized using Robust Multiarray Averaging (RMA).
 
Submission date Apr 23, 2014
Last update date Apr 30, 2014
Contact name Kenneth N Ross
E-mail(s) Kenneth.Ross@dfci.harvard.edu
Organization name Dana-Farber Cancer Institute
Department Pediatric Oncology
Street address 450 Brookline Ave., Rm M640
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL8321
Series (1)
GSE57002 Mutant IDH inhibits HNF4a to disrupt hepatocyte differentiation and promote cholangiocarcinoma.

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
1415670_at 1291.961
1415671_at 1491.903
1415672_at 3589.821
1415673_at 2825.583
1415674_a_at 1881.529
1415675_at 847.635
1415676_a_at 3853.808
1415677_at 977.509
1415678_at 1968.241
1415679_at 3243.14
1415680_at 2330.189
1415681_at 2660.362
1415682_at 583.65
1415683_at 4115.955
1415684_at 537.338
1415685_at 1019.493
1415686_at 2042.168
1415687_a_at 2982.661
1415688_at 2750.194
1415689_s_at 707.938

Total number of rows: 22690

Table truncated, full table size 427 Kbytes.




Supplementary file Size Download File type/resource
GSM1372817_NB20112111343.CEL.gz 2.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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