NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2199477 Query DataSets for GSM2199477
Status Public on Dec 31, 2017
Title (b) Liver from LDR(20mGy/d)-irradiated mice without HCA 9
Sample type RNA
 
Source name Liver from LDR(20mGy/d)-irradiated mice without HCA
Organism Mus musculus
Characteristics strain: B6C3F1
gender: Female
disease state: control
treatment: irradiated
tissue: liver
Treatment protocol Female B6C3F1 mice from 8 weeks of age were irradiated for 400 d at LDR at 0.02 Gy/22 h/d (0.00091 Gy/h) 137Cs-γ rays (74 GBq), in which the total doses was 8 Gy. And the chronically irradiated mice for 400 d (8 Gy) were bled in the SPF condition without irradiation for 100, 200 and 300 d, in which the total days were 500, 600, 700 d after beginning of irradiation, respectively.
Extracted molecule total RNA
Extraction protocol A piece of livers with adenomas or non-adenoma were homogenized in Trizol (Invitrogen, Carlsbad, CA, USA) reagent within 2 h after death.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the Quickamp lebeling kit (Agilent) according to the manufacturer's instructions (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 40°C for 120 minutes in a reaction volume of 100 ml containing 1x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides, (Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).
Description (b) Liver from LDR(20mGy/d)-irradiated mice without HCA 9
Data processing The scanned images were analyzed with Feature Extraction Software 13.0 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Jun 14, 2016
Last update date Dec 31, 2017
Contact name Takashi Sugihara
E-mail(s) sugihara@ies.or.jp
Organization name Institute for Environmental Sciences
Department Radiobiology
Street address 2-121 Hacchazawa
City Rokkasho
State/province Aomori
ZIP/Postal code 039-3213
Country Japan
 
Platform ID GPL7202
Series (1)
GSE83318 Gene expressions of mice hepatocellular adenoma, which correlated with low-dose-rate gamma ray radiation dependent inflammatory response

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_52_P616356 0.74220085
A_52_P580582 -0.67732286
A_52_P403405 0.53238106
A_52_P819156 -0.38003588
A_51_P331831 -0.41734695
A_51_P430630 0.74946976
A_52_P502357 0.74833965
A_52_P299964 0.72554207
A_51_P356389 0.602231
A_52_P684402 0.822278
A_51_P414208 0.73743343
A_51_P280918 0.2650633
A_52_P613688 -0.8280878
A_52_P258194 0.7241287
A_52_P229271 0.67558
A_52_P214630 -0.35578585
A_52_P579519 0.35599566
A_52_P979997 0.7206912
A_52_P453864 0.7132664
A_52_P655842 0.6392808

Total number of rows: 41265

Table truncated, full table size 961 Kbytes.




Supplementary file Size Download File type/resource
GSM2199477_US84300232_251486836501_S01_GE1_107_Sep09_1_1.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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