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Sample GSM487636 Query DataSets for GSM487636
Status Public on Dec 19, 2009
Title Interstitial leukocytes from WT C57Bl6 mice exposed to silica, replicate 1
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 1 of 2, WT silica.
WT-si-1
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 0.359362504
A_51_P100063 0.397365614
A_51_P100099 -0.292501173
A_51_P100155 -0.320949022
A_51_P100174 -0.26548445
A_51_P100181 -0.067750767
A_51_P100227 -0.36443186
A_51_P100246 -0.250019281
A_51_P100289 -0.150400573
A_51_P100298 -0.186619974
A_51_P100327 0.135899885
A_51_P100347 -0.016841149
A_51_P100470 0.011032967
A_51_P100505 0.221103151
A_51_P100565 0.339251238
A_51_P100573 0.115091771
A_51_P100787 -0.207943673
A_51_P100828 -0.024135312
A_51_P100852 0.135137564
A_51_P100856 -0.436391168

Total number of rows: 16251

Table truncated, full table size 402 Kbytes.




Supplementary file Size Download File type/resource
GSM487636.gpr.gz 6.2 Mb (ftp)(http) GPR
Processed data included within Sample table

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