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Sample GSM1372811 Query DataSets for GSM1372811
Status Public on Apr 30, 2014
Title IHCC_Vector_Collagen_Rep2
Sample type RNA
 
Source name HBs_empty vector controls_collagen-coated plates
Organism Mus musculus
Characteristics cell type: hepatoblasts (HBs) from E14 WT mouse
genotype/variation: expressing empty vector controls
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_Vect_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 1257.858
1415671_at 1571.077
1415672_at 3453.734
1415673_at 2958.217
1415674_a_at 1952.529
1415675_at 880.862
1415676_a_at 3905.374
1415677_at 960.314
1415678_at 1890.619
1415679_at 3216.163
1415680_at 2190.815
1415681_at 2805.903
1415682_at 608.814
1415683_at 3888.057
1415684_at 520.746
1415685_at 960.061
1415686_at 1953.432
1415687_a_at 3336.908
1415688_at 2826.113
1415689_s_at 703.434

Total number of rows: 22690

Table truncated, full table size 427 Kbytes.




Supplementary file Size Download File type/resource
GSM1372811_NB20112111340.CEL.gz 2.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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