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Sample GSM1372814 Query DataSets for GSM1372814
Status Public on Apr 30, 2014
Title IHCC_IDH1_mutant_R132C_Collagen_Rep1
Sample type RNA
 
Source name HBs_R132C mutant IDH1_collagen-coated plates
Organism Mus musculus
Characteristics cell type: hepatoblasts (HBs) from E14 WT mouse
genotype/variation: expressing R132C mutant IDH1
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_IDH1_mut_R132C_Collagen_1
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 1177.818
1415671_at 1452.835
1415672_at 3134.856
1415673_at 1557.537
1415674_a_at 1754.922
1415675_at 881.598
1415676_a_at 3892.275
1415677_at 689.04
1415678_at 2029.606
1415679_at 3296.865
1415680_at 2400.628
1415681_at 2507.532
1415682_at 685.776
1415683_at 3874.676
1415684_at 566.387
1415685_at 894.738
1415686_at 1855.395
1415687_a_at 3218.104
1415688_at 2581.818
1415689_s_at 603.421

Total number of rows: 22690

Table truncated, full table size 427 Kbytes.




Supplementary file Size Download File type/resource
GSM1372814_NB20112111337.CEL.gz 2.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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