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Sample GSM1372821 Query DataSets for GSM1372821
Status Public on Apr 30, 2014
Title IHCC_Vector_NoCollagen_Rep2
Sample type RNA
 
Source name HBs_empty vector controls_uncoated plates
Organism Mus musculus
Characteristics cell type: hepatoblasts (HBs) from E14 WT mouse
genotype/variation: expressing empty vector controls
culture plate: uncoated 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_NoCollagen_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) [email protected]
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 1133.104
1415671_at 3092.737
1415672_at 4194.969
1415673_at 625.235
1415674_a_at 1609.27
1415675_at 952.797
1415676_a_at 3701.207
1415677_at 978.657
1415678_at 1826.223
1415679_at 4431.46
1415680_at 1302.898
1415681_at 2958.746
1415682_at 578.953
1415683_at 3268.614
1415684_at 438.252
1415685_at 1024.375
1415686_at 1766.941
1415687_a_at 5127.387
1415688_at 3164.863
1415689_s_at 838.187

Total number of rows: 22690

Table truncated, full table size 427 Kbytes.




Supplementary file Size Download File type/resource
GSM1372821_39_PRTplus2.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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