NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM969520 Query DataSets for GSM969520
Status Public on Aug 01, 2012
Title Mix2_3
Sample type RNA
 
Source name Mouse skin exposed to PAH mixture 2 (Mix2), biological rep3
Organism Mus musculus
Characteristics treatment: 1 mg diesel particulate extract + 1 mg coal tar extract
tissue: skin
strain: FVB/N
Treatment protocol At 7.5 weeks of age, mice were shaved on their dorsal surface and allowed to rest 48 h to confirm that animals were in the resting phase of the hair growth cycle. The following initiation treatments were applied to groups of mice (N=4 or 5 biological replicates) by slowly pipetting solutions on the shaved area; toluene vehicle control (200 μl), benzo[a]pyrene (BAP) 400 nmol (100 μg), dibenzo[def,p]chrysene (DBC) 4 nmol (1.2 μg), or 1 of 3 PAH mixtures: Mix 1 (1 mg diesel particulate extract), Mix 2 (1 mg diesel particulate extract + 1 mg coal tar extract), or Mix 3(1 mg diesel particulate extract + 1 mg coal tar extract + 2 mg cigarette smoke condensate).
Extracted molecule total RNA
Extraction protocol In order to eliminate RNase degradation, epidermis and dermis layers were kept intact, removed as one piece and snap frozen in liquid nitrogen. A 1-cm2 section of frozen skin was placed in a 15-ml sterile, disposable conical homogenizer, VWR Scientific Inc. (San Francisco, CA.) and homogenized in 2 ml Trizol® reagent. RNA was extracted according to the manufacturer’s instructions followed by a clean-up step using an RNeasy® mini kit, Qiagen Corp., Valencia, CA.
Label Cy3
Label protocol The RNA was labeled with Agilent’s 2 color Quickamp kit.
 
Hybridization protocol Samples were hybridized to the Agilent 8X60 K mouse array following manufacturer instructions.
Scan protocol Agilent Technologies Scanner G2505C 3um 20bit
Description Gene expression in mouse skin 12 hr post-initiation
Data processing Raw Agilent intensity data were background subtracted and quantile-normalized by RMA summarization as described by (Bolstad et al., 2003). Statistical analysis was performed by one-way ANOVA for unequal variances (Welch’s ANOVA) with Tukey’s posthoc test and 5% FDR.
 
Submission date Jul 18, 2012
Last update date Aug 01, 2012
Contact name Susan C. Tilton
E-mail(s) Susan.Tilton@oregonstate.edu
Organization name Oregon State University
Department AG Envr & Molec Toxicology
Street address 1007 ALS Bldg
City Corvallis
State/province OR
ZIP/Postal code 97331
Country USA
 
Platform ID GPL10787
Series (1)
GSE39455 Polycyclic aromatic hydrocarbons as skin carcinogens: Comparison of benzo[a]pyrene, dibenzo[def,p]chrysene and three environmental mixtures in the FVB/N mouse

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
(+)E1A_r60_1 3.9846761
(+)E1A_r60_3 5.7928185
(+)E1A_r60_a104 7.4762506
(+)E1A_r60_a107 7.9109745
(+)E1A_r60_a135 5.8569098
(+)E1A_r60_a20 7.122984
(+)E1A_r60_a22 6.6751704
(+)E1A_r60_a97 7.300539
(+)E1A_r60_n11 8.82413
(+)E1A_r60_n9 7.287688
3xSLv1 3.1919143
A_30_P01017425 6.9239817
A_30_P01017426 6.640888
A_30_P01017427 4.6863065
A_30_P01017428 8.123493
A_30_P01017429 3.387511
A_30_P01017430 7.8874917
A_30_P01017431 4.701206
A_30_P01017432 6.2157693
A_30_P01017433 5.070749

Total number of rows: 55821

Table truncated, full table size 1283 Kbytes.




Supplementary file Size Download File type/resource
GSM969520_US10130359_252800511656_S01_GE1_107_Sep09_1_4.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap