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Sample GSM487637 Query DataSets for GSM487637
Status Public on Dec 19, 2009
Title Interstitial leukocytes from WT C57Bl6 mice exposed to silica, replicate 2
Sample type RNA
 
Channel 1
Source name WT C57 lung interstitial leukocytes
Organism Mus musculus
Characteristics strain: C57Bl/6
genotype: wild-type
tissue: lung
cell type: interstitial leukocytes
age: 6-8 weeks
treatment: silica
Treatment protocol For “chronic” exposure studies, Rag1-/- NK-depleted and C57Bl/6 wild-type mice were anesthetized with ketamine (80 mg/kg) and instilled i.n. with either 25 μl of sterile saline, 1 mg crystalline silica (SiO2) or 0.5 mg titanium dioxide (TiO2) suspended in 25 μl of sterile saline once a week for four weeks.
Growth protocol Rag1-/- mice were injected i.p. with 300 μg of anti-NK1.1 mAb on days -6, -3, and -1 prior to the first i.n. instillation (day 0). NK cell depletion was maintained via weekly injections of 300 μg of anti-NK1.1 mAb throughout the course of the study, which was administered two days prior to particle exposure.
Extracted molecule total RNA
Extraction protocol The lungs were asceptically removed, cut away from the heart, and placed in ice cold sterile phosphate-buffered saline (PBS, pH 7.4). Thereafter, the lungs were minced into small pieces and incubated in complete RPMI 1640 culture medium supplemented with 10% FCS, antibiotic/antimycotic solution, β-mercaptoethanol, and sodium pyruvate containing 1 mg/ml collagenase IA with 1 µl DNAase I during 2 hours at 37oC. Digested lungs were further disrupted by gently pushing the tissue through a 70 μm cell strainer. Enzymatic action was terminated by adding excess RPMI medium and pelleting by centrifugation at 1500 rpm for 5 minutes at 4oC. Leukocytes were isolated by centrifugation over a 40-70% Percol gradient. Total RNA was isolated using Trizol according to manufacturer's protocol, followed by Qiagen RNeasy RNA cleanup with DNase digest.
Label Cy5
Label protocol Agilent Quick-Amp Labeling Kit, Dual Color.
 
Channel 2
Source name Universal Mouse Reference RNA
Organism Mus musculus
Characteristics supplier: Stratagene
Treatment protocol For “chronic” exposure studies, Rag1-/- NK-depleted and C57Bl/6 wild-type mice were anesthetized with ketamine (80 mg/kg) and instilled i.n. with either 25 μl of sterile saline, 1 mg crystalline silica (SiO2) or 0.5 mg titanium dioxide (TiO2) suspended in 25 μl of sterile saline once a week for four weeks.
Growth protocol Rag1-/- mice were injected i.p. with 300 μg of anti-NK1.1 mAb on days -6, -3, and -1 prior to the first i.n. instillation (day 0). NK cell depletion was maintained via weekly injections of 300 μg of anti-NK1.1 mAb throughout the course of the study, which was administered two days prior to particle exposure.
Extracted molecule total RNA
Extraction protocol The lungs were asceptically removed, cut away from the heart, and placed in ice cold sterile phosphate-buffered saline (PBS, pH 7.4). Thereafter, the lungs were minced into small pieces and incubated in complete RPMI 1640 culture medium supplemented with 10% FCS, antibiotic/antimycotic solution, β-mercaptoethanol, and sodium pyruvate containing 1 mg/ml collagenase IA with 1 µl DNAase I during 2 hours at 37oC. Digested lungs were further disrupted by gently pushing the tissue through a 70 μm cell strainer. Enzymatic action was terminated by adding excess RPMI medium and pelleting by centrifugation at 1500 rpm for 5 minutes at 4oC. Leukocytes were isolated by centrifugation over a 40-70% Percol gradient. Total RNA was isolated using Trizol according to manufacturer's protocol, followed by Qiagen RNeasy RNA cleanup with DNase digest.
Label Cy3
Label protocol Agilent Quick-Amp Labeling Kit, Dual Color.
 
 
Hybridization protocol Agilent Gene Expression Hybridization Kit.
Scan protocol Axon GenePix 4000B scanner, Axon GenePix Pro 5.0 software.
Description Biological replicate 2 of 2, WT silica.
WT-si-2
Data processing Axon GenePix Pro 5.0, normalization using a LOWESS R script written by Terry Speed, Microsoft Excel. Matrix data was filtered to include only non-control genes and genes present above background in at least 2 of 4 replicates for wild-type or RagKO data.
 
Submission date Dec 18, 2009
Last update date Dec 18, 2009
Contact name Corbin Schwanke
E-mail(s) corbin.schwanke@umontana.edu
Phone 406-243-4571
Fax 406 243-4571
Organization name University of Montana
Department Biomedical and Pharmaceutical Sciences
Lab The Center for Environmental Health Sciences
Street address
City Missoula
State/province MT
ZIP/Postal code 59801
Country USA
 
Platform ID GPL7202
Series (1)
GSE19563 Gene expression response to silica treatment in wild-type C57 black 6 mice vs Rag1 knockout, NK-depleted mice

Data table header descriptions
ID_REF
VALUE Normalized log10 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
A_51_P100034 0.357587065
A_51_P100063 0.384608026
A_51_P100099 -0.300383812
A_51_P100155 -0.283871301
A_51_P100174 -0.048962374
A_51_P100181 -0.168195141
A_51_P100227 -0.44481136
A_51_P100246 -0.282331007
A_51_P100289 -0.112220398
A_51_P100298 -0.21212029
A_51_P100327 0.092380562
A_51_P100347 0.019538973
A_51_P100470 -0.014577137
A_51_P100505 0.151627001
A_51_P100565 0.272845164
A_51_P100573 0.144042156
A_51_P100787 -0.133313713
A_51_P100828 -0.103538695
A_51_P100852 0.12745944
A_51_P100856 -0.502823894

Total number of rows: 16251

Table truncated, full table size 402 Kbytes.




Supplementary file Size Download File type/resource
GSM487637.gpr.gz 6.1 Mb (ftp)(http) GPR
Processed data included within Sample table

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