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Sample GSM513586 Query DataSets for GSM513586
Status Public on Oct 22, 2010
Title normal thymus from control mouse_sample_TL20070522_1_2_C2
Sample type RNA
 
Source name normal whole thymus tissue, at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size
Organism Mus musculus
Characteristics gender: female
strain: FVB
genotype: control mice transgenic for TetO-NeuNT only and littermates of the bitransgenic mice
tissue: normal whole thymus tissue, at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size
Treatment protocol All mice received doxycycline (2 mg/mL + 5% sucrose) in the drinking water starting at 8 weeks of age. Doxycycline was used to induce tumor development in the bitransgenic mice and breast tumors were allowed to develop to 1.0 cm in diameter after which each tumor-bearing mouse and its corresponding control littermate were euthanized by CO2 inhalation. Tissue samples were collected when the tumors reached ~1 cm size and the samples were snap-frozen in liquid nitrogen.
Growth protocol All mouse work was performed under IACUC regulations as approved by the Fred Hutchinson Cancer Research Center's animal use committee. For these studies, a doxycycline-inducible, bitransgenic MMTV-rtTA/TetO-NeuNT (Her2/Neu) mouse model was used. Corresponding control mice were transgenic for TetO-NeuNT only and were littermates of the bitransgenic mice. The procedures for animal husbandry and tissue and plasma sample collection were previously reported in Whiteaker J.R., et al., J. Proteome Res. 2007, 10, 3962-3975 and Kelly-Spratt, K.S., et al., J. Proteome Res. 2008, 8, 3613-3618. Briefly, all mice were fed standard laboratory chow (Harland Teklad, 8664) and acidified water ad libitum and kept on a 12 hour light-dark cycle.
Extracted molecule total RNA
Extraction protocol The tissues from thymus, spleen, liver, blood cells (blood with plasma fraction removed), and breast were homogenized, and total RNA was isolated using a standard Trizol (Invitrogen, Carlsbad, CA) and chloroform extraction protocol.
Label biotin
Label protocol Purified total RNA was normalized to 125ng/ul and reverse transcribed to produce double-stranded cDNA which was amplified, producing biotin-labeled cRNA using the GeneChip HT One-Cycle Target Labeling and Controls Kit (Affymetrix, Santa Clara, CA.)
 
Hybridization protocol Biotinylated cRNA (600 ng/ul) was hybridized to GeneChip® Mouse 430 2.0 arrays (Affymetrix, Santa Clara, CA) following the manufacturer’s suggested protocols.
Scan protocol The arrays were washed and stained using a GeneChip® Fluidics Station and scanned using a GeneChip® Scanner 3000.
Description Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_C1
sample ID: 011906218
sample ID of_age- and cage-matched_mouse: 011906208
Data processing Two sequential quality control checks were implemented to evaluate whether to include results from each of the GeneChips. In the first step, recommendations made by Affymetrix were followed.(Zweig, M. H.; Campbell, G. Clin. Chem. 1993, 39, 561-577) In the second step, we used the affyQCReport and affyPLM software in the Bioconductor package (http://www.bioconductor.org/) to search for poor-quality chips.(Pyeon, D.; et al. Cancer Res. 2007, 67, 4605-4619) In total, 250 chips from both normal and cancer samples from 5 tissues passed these two steps of quality control evaluation. After passing the quality control checks, the DNA microarray data of each separate tissue type were subjected to a quartile normalization step (using Gene Pattern software version 3.0) where intensities of different arrays (but from the same tissue type) were adjusted to the same scale so that the intensity levels from the different arrays could be compared with one another. The normalization was performed on log2 transformed data.
 
Submission date Feb 22, 2010
Last update date Oct 22, 2010
Contact name Regine M Schoenherr
Organization name Fred Hutchinson Cancer Research Center
Street address 1100 Fairview Ave N, LE-360
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
 
Platform ID GPL1261
Series (1)
GSE20465 Her2/Neu breast cancer mouse model whole tissue transcriptome

Data table header descriptions
ID_REF
VALUE Quartile normalized original signal intensity (converted back from log2 values after normalization)

Data table
ID_REF VALUE
1415670_at 1303.654016
1415671_at 3421.870698
1415672_at 4946.928097
1415673_at 1203.232044
1415674_a_at 1643.752632
1415675_at 701.3385219
1415676_a_at 4637.071658
1415677_at 1273.827447
1415678_at 3213.19945
1415679_at 3783.367334
1415680_at 1693.266294
1415681_at 2064.366454
1415682_at 1175.748129
1415683_at 4129.229178
1415684_at 1109.304786
1415685_at 1301.103778
1415686_at 2162.833936
1415687_a_at 4618.594414
1415688_at 2735.61433
1415689_s_at 1586.382485

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM513586_TL20070522_1_2_C2.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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