NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4618932 Query DataSets for GSM4618932
Status Public on Sep 07, 2021
Title TREATED_rep3 (cobalt)
Sample type RNA
 
Source name lung, cobalt treated tumor
Organism Mus musculus
Characteristics group: cobalt_Treated Tumor
Treatment protocol Cobalt metal dust was produced by OMG Kokkola Chemicals Oy (Kokkola, Finland) and was provided by the Cobalt Development Institute via PEL Technologies in one lot (P32 3040-1) that was used in the 2-week, 3-month, and 2-year studies. Groups of 50 male and 50 female mice were exposed to cobalt metal particulate aerosol by inhalation at concentrations of 0, 1.25, 2.5, or 5 mg/m3, 6 hours plus T90 (12 minutes) per day, 5 days per week for up to 105 weeks.
Growth protocol At the start of the study, the animals were 5–6 weeks of age. The animals were housed 2 per cage. Tap water and NTP-2000 diet (Zeigler Brothers, Inc. Gardners, PA) were made available ad libitum. The care of animals on this study was according to National Institutes of Health (NIH) procedures as described in the ‘‘The U.S. Public Health Service Policy on Humane Care and Use of Laboratory Animals,’’ available from the Office of Laboratory Animal Welfare, NIH, Department of Health and Human Services, RKLI, Bethesda, MD or online at http://grants.nih.gov/grants/olaw/olaw.htm#pol.
Extracted molecule total RNA
Extraction protocol The lung was harvested and weighed, and then, a representative sections are collected and fixed in 10 % neutral buffered formalin for histology. Hematoxylin and eosin (H&E)-stained sections (5 μm) were examined by a board certified pathologist. Selected lung tumors are dissected from the remaining lung parenchyma and flash-frozen in liquid nitrogen and stored at −80 °C until RNA extraction. RNA was extracted from frozen samples using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A, Carlsbad, CA) according to the manufacturer’s protocol. RNA concentration and quality were measured on a Bioanalyzer (Agilent Technologies, Santa Clara, CA). Samples were aliquoted and stored at −80 °C until they were analyzed for gene expression studies.
Label biotin
Label protocol One hundred nanograms of total RNA was amplified as directed in the Affymetrix 3′ IVT Plus kit protocol. Fifteen micrograms of amplified biotin-aRNAs was fragmented, and 12.5 μg was hybridized to each array for 16 h at 45 °C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.
 
Hybridization protocol Labeled cRNA was fragmented and hybridized to the Affymetrix Rat Genome 230 2.0 GeneChip arrays (Affymetrix, Santa Clara, CA). Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
Scan protocol Affymetrix Scanner 3000
Description cobalt treated tumor M. musculus sample
Data processing Data were processed using R/affy software. In brief, the RMA method adjusts the background of perfect match (PM) probes, applies a quantile normalization of the corrected PM values, and calculates final expression measures with the Tukey median polish algorithm. Data were normalized across all three groups.
 
Submission date Jun 16, 2020
Last update date Sep 07, 2021
Contact name Keith Shockley
Organization name NIEHS
Street address 111 TW Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL1261
Series (1)
GSE152630 Cobalt Induced Oxidative Stress Contributes to Alveolar/Bronchiolar Carcinogenesis in B6C3F1/N Mice

Data table header descriptions
ID_REF
VALUE RMA expression measures from R/affy package

Data table
ID_REF VALUE
1415670_at 10.20631104
1415671_at 11.02816987
1415672_at 10.6198614
1415673_at 7.246306446
1415674_a_at 9.378708156
1415675_at 8.906854651
1415676_a_at 11.28365037
1415677_at 9.008027732
1415678_at 10.59233023
1415679_at 11.55677542
1415680_at 8.867840094
1415681_at 9.697181821
1415682_at 8.378651653
1415683_at 11.03937323
1415684_at 8.315697104
1415685_at 8.220044581
1415686_at 9.751223354
1415687_a_at 12.50675809
1415688_at 10.24801439
1415689_s_at 8.68001945

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM4618932_8668_496_Treated_Rep3_Mouse430_2_.CEL.gz 3.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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