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Sample GSM1580421 Query DataSets for GSM1580421
Status Public on Jun 25, 2015
Title day7_control_rep5
Sample type RNA
 
Source name C57BL/6, control, day 7, rep5
Organism Mus musculus
Characteristics tissue: whole blood
strain: C57BL/6
Treatment protocol C57BL/6 mice (approximately 10-12 weeks old, 25-30 g) were received from Charles River Laboratories (Frederick, MD) and were quarantined for 14 days prior to group assignment by body weight stratification for randomization into the study. Animals were administered 90-Strontium intravenously by tail vein injection with 200 ± 0.3 kBq 85/90SrCl2 solution in a volume of 0.05 mL
Extracted molecule total RNA
Extraction protocol All blood samples were collected by cardiac puncture in a sterile hood. For each animal ~0.4 mL of blood was collected into 2 mL of PAXgene Blood RNA stabilization and lysis solution (PreAnalytix GmBH, catalog#762165), mixed thoroughly and shipped at 4ºC in temperature-stabilized containers. They were stored for a further 24 hour at 4ºC, and then incubated at room temperature for a minimum of 2 hours before proceeding with RNA isolation. RNA was purified following the PAXgene Blood RNA kit recommended protocol with on-column DNaseI treatment.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared with the One-Color Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND1000 Spectrophotometer
 
Hybridization protocol 1.6 microgram of cRNA, >9 pmol Cy3 per microgram cRNA was fragmented and hybridized (17 hours with rotation at 65°C) to Agilent Whole Mouse Genome Microarrays 4X44K v2 (G4846A), and then washed using the Gene Expression Hybridization Kit and GE Wash Buffers as recommended by Agilent
Scan protocol Slides were scanned with the Agilent DNA Microarray Scanner (G2505B), and the images were analyzed (Agilent Feature Extraction Software ver. 10.7) with default parameters for background correction and flagging non-uniform features.
Description Gene expression in mouse whole blood at day 7
Data processing The scanned images were analyzed with Feature Extraction Software 10.7 (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 Jan 08, 2015
Last update date Jun 26, 2015
Contact name Shanaz Adi Ghandhi
E-mail(s) [email protected]
Phone 212-3053911
Organization name Columbia University Medical Center
Department Center for Radiological Research
Lab VC11-237
Street address 630, W 168th street
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platform ID GPL11202
Series (1)
GSE64775 Effect of 90Sr internal emitter on gene expression in mouse blood

Data table header descriptions
ID_REF
VALUE Normalized log transformed intensities

Data table
ID_REF VALUE
GE_BrightCorner 15.16260147
DarkCorner 3.826560974
A_55_P1989846 6.566260338
A_55_P2022211 3.456744194
A_55_P1964375 6.643479824
A_51_P207591 1.85581398
A_55_P2404223 3.952969074
A_51_P343900 7.694723129
A_51_P487813 5.068446159
A_55_P1957209 6.869542122
A_55_P1958431 4.153700829
A_55_P2111153 6.269890785
A_51_P210560 8.206566811
A_55_P2048493 4.707821846
A_55_P1996087 7.389156342
A_51_P112237 3.75477314
A_55_P1958246 7.222448349
A_52_P546635 4.290987492
A_66_P126300 6.160275936
A_55_P2005898 4.629906654

Total number of rows: 14208

Table truncated, full table size 345 Kbytes.




Supplementary file Size Download File type/resource
GSM1580421_Sr_mouse_009.txt.gz 8.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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