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Sample GSM787705 Query DataSets for GSM787705
Status Public on Aug 07, 2012
Title liver tumor 8
Sample type RNA
 
Channel 1
Source name HCC in miR-122 KO male mice
Organism Mus musculus
Characteristics tissue: HCC liver tumor
genotype: miR-122 KO
genetic background: C57BL/6J and 129S/Svj mixed
Growth protocol Liver tumors from miR-122 knockout mice and livers from age-matched WT mice
Extracted molecule total RNA
Extraction protocol RNA was extracted using miRVana kit (Invitrogen) followed by further purification using RNeasy kit (Aquagen).
Label Cy5
Label protocol Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Version 6.5, May 2010
 
Channel 2
Source name miR-122 floxed male mouse
Organism Mus musculus
Characteristics tissue: liver
genotype: miR-122 floxed
genetic background: C57BL/6J and 129S/Svj mixed
Growth protocol Liver tumors from miR-122 knockout mice and livers from age-matched WT mice
Extracted molecule total RNA
Extraction protocol RNA was extracted using miRVana kit (Invitrogen) followed by further purification using RNeasy kit (Aquagen).
Label Cy3
Label protocol Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Version 6.5, May 2010
 
 
Hybridization protocol Arrays were hybridized for 17 hours at 65 degrees Celsius.
Scan protocol Scanned with Agilent G2505C Microarray Scanner using the AgilentG3_GX_2Color protocol
Description Biological Replicate 8
Data processing The information about each probe on the array was extracted from the image data using Agilent Feature Extraction 10.9 (FE). This data is stored in the FE “.txt” files. The raw intensity values from these files is imported into the mathematical software package “R”, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house by Peter White specifically for this analysis.
 
Submission date Aug 29, 2011
Last update date Aug 07, 2012
Contact name kalpana ghoshal
E-mail(s) kalpana.ghoshal@osumc.edu
Phone 614-292-8865
Fax 614-688-5600
Organization name The Ohio State University
Department Molecular and Cellular Biochemistry
Street address 420 W. 12th Avenue
City Columbus
State/province OH
ZIP/Postal code 43210
Country USA
 
Platform ID GPL13912
Series (1)
GSE31731 Gene expression profile of HCCs developed in miR-122 knockout mice compared to age-matched wild type mice

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 7.014814728e-002
2 0.000000000e+000
3 0.000000000e+000
4 0.000000000e+000
5 -2.298804596e-001
6 0.000000000e+000
7 0.000000000e+000
8 -2.836229116e-001
9 0.000000000e+000
10 0.000000000e+000
11 0.000000000e+000
12 0.000000000e+000
13 -2.166607104e-001
14 -9.470128661e-002
15 0.000000000e+000
16 0.000000000e+000
17 -2.556300674e-001
18 -2.126418622e-001
19 1.238335586e-001
20 -2.608347743e-001

Total number of rows: 62976

Table truncated, full table size 1427 Kbytes.




Supplementary file Size Download File type/resource
GSM787705_US85103615_252800512154_S01_GE2_109_Feb10_2_4.txt.gz 6.0 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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