NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3753946 Query DataSets for GSM3753946
Status Public on Jul 26, 2019
Title lung, 620B_600_Rm300
Sample type RNA
 
Source name lung, 40ug MWCNT, 12 mo
Organism Mus musculus
Characteristics strain: C57BL/J6
treatment: 40ug MWCNT
time: 12 mo
tissue: lung
Treatment protocol Each component consisted of 8 mice per exposure group (dispersion media [DM, negative control]; 1, 10, 40, or 80 μg MWCNT; 120 μg crocidolite asbestos [positive control]) to be sacrificed at 1, 6 or 12 months post-exposure, for a total of 144 mice.
Growth protocol Individual mice were housed 1 per cage in polycarbonate isolator ventilated cages and provided HEPA-filtered air with fluorescent lighting from 0700 to 1900 hr. Autoclaved Alpha-Dri virgin cellulose chips and hardwood Beta-chips were used as bedding. Mice were monitored to be free of adventitous viral pathogens, parasites, mycoplasms, Helicobacter, and CAR Bacillus.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from mouse lung tissue using a mirVana miRNA Isolation Kit from Ambion per the manufacturer's protocol.
Label Oyster-550 fluorescent dye
Label protocol The total RNA with was DNAse digested and low-molecular weight (LMW) RNA was isolated by ultrafiltration through YM-100 columns (Millipore) and subsequent purification using the RNeasy MinElute Clean-Up Kit (Qiagen). The LMW RNA samples were 3’-end labeled with Oyster-550 fluorescent dye using the Flash Tag RNA labeling Kit (Genisphere).
 
Hybridization protocol Labeled LMW RNA samples were hybridized to the MicroRNA microarrays according to conditions recommended in the Flash Tag RNA labeling Kit manual.
Scan protocol The microarrays were scanned on an Axon Genepix 4000B scanner, and data was extracted from images using GenePix V4.1 software.
Description raw data file: 2013-08-23_19718620_600PMT_5um_0532.txt
Array B (blocks 9-16)
Data processing Data for 4 arrays were extracted from a single microarray image into a single text file using GenePix version 4.1 software. The raw text files were split into four subfiles based on block assignment, namely blocks 1-8 contained data for array A, blocks 9-16 contained data for array B, blocks 17-24 contained data for array C, and blocks 25-32 contained data for array D. Spot intensities were obtained for the 10240 features on each microarray by subtracting the median local background from the median local foreground for each spot. Visually flagged spots were removed prior to averaging and normalizing.The 95th percentile of the negative control spots was also calculated for each array. The spot intensities and 95th percentile of negative controls (TPT95) were transformed by taking the log (base 2) of each value. The detection threshold (T) for each microarray was computed by summing five times the standard deviation of the background signal and the 10% trim mean of the negative control spots. The mean probe intensities for each of the probes on each array were then determined by averaging the triplicate spot intensities. Spots that have an average saturated signal were removed prior to normalization. The normalization factor (N) for each microarray was determined by obtaining the 20% trim mean of the non-saturated human probes above threshold in all samples. The log2-transformed spot intensities for all features were normalized, by subtracting N from each spot intensity, and scaled by adding the grand mean of N across all microarrays.
 
Submission date May 07, 2019
Last update date Jul 26, 2019
Contact name Nancy Lan Guo
E-mail(s) lguo@hsc.wvu.edu
Phone 3042936455
Organization name West Virginia University
Department Occupational and Environmental Health Sciences
Lab Mary Babb Randolph Cancer Center/Guo Laboratory
Street address 2816 Health Sciences Center
City Morgatown
State/province WV
ZIP/Postal code 26506-9300
Country USA
 
Platform ID GPL26525
Series (2)
GSE130790 miRNA profiling of lung tissues exposed to MWCNT
GSE131123 miRNA profiling of MWCNT exposed mice

Data table header descriptions
ID_REF
VALUE Normalized Signal Intensity

Data table
ID_REF VALUE
1001 10.49
1003 8.58
1008 5.45
1009 5.79
1012 7.27
1014 10.44
1015 10.23
1021 6.67
1028 4.25
1032 4.65
1038 4.97
1047 5.13
1052 4.49
1063 15.03
1064 14.14
1068 15.60
1082_3 10.28
1084 7.51
1092 13.10
1094 13.58

Total number of rows: 1223

Table truncated, full table size 17 Kbytes.




Supplementary data files not provided
Processed data are available on Series record

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