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Sample GSM2790259 Query DataSets for GSM2790259
Status Public on May 31, 2018
Title Whole Blood 16hr after 1Gy dose rep 2
Sample type RNA
 
Source name Whole Blood 16hr after 1Gy dose
Organism Mus musculus
Characteristics strain/background: C57BL/6
gender: female
age: six to eight weeks
tissue: whole blood
treatment: 1Gy gamma rays
time point: 16hr
Treatment protocol Whole body irradiation done with X-rays using the Small Animal Radiation Research Platform (SARRP Xstrahl Ltd.). Mice were placed in plastic containers and exposed to a single surface dose of 0-12 Gy with a dose rate of 1.05 Gy/min. Control mice (0 Gy) were placed in the same plastic container as the irradiated mice and sham irradiated. 3 animals/dose/time-point have been included in the study.
Extracted molecule total RNA
Extraction protocol RNA was extracted and purified using Ribopure (Ambion) RNA isolation.
Label Alexa 555
Label protocol Labeled cRNA was prepared from total RNA samples. Briefly, the Poly(A)+ RNA population within total RNA was amplified using MessageAMP II (Applied Biosystems, Foster City, CA). After a second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Biotin-11-UTP. The quantity and quality of the cRNA were assayed by spectrophotometry and on the Agilent Bioanalyzer.
 
Hybridization protocol 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Mouse Genome microarrays 8x60K v1 Design ID 028005 or v2 Design ID 074809 (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.
Scan protocol Rinsed and dried arrays were scanned with an Agilent G2505C Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.
Description 16hr_1Gy_2
Data processing Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA). Only the 30,000+ probes that are printed on both arrays (Agilent-028005, Agilent-074809) are reported.
 
Submission date Sep 21, 2017
Last update date May 31, 2018
Contact name Michael Falduto
E-mail(s) mfalduto@genusbiosystems.com
Phone 847-291-9602
Organization name GenUs BioSystems, Inc.
Street address 1808 Janke, Unit M
City Northbrook
State/province IL
ZIP/Postal code 60062
Country USA
 
Platform ID GPL21163
Series (1)
GSE104121 Radiation-induced molecular alterations after whole body irradiation in a mouse model

Data table header descriptions
ID_REF
VALUE Intensity values are normalized to the 75th percentile intensity of above background probes on each array.

Data table
ID_REF VALUE
A_52_P447424 0.236
A_55_P2036774 0.058
A_55_P2375880 0.049
A_55_P2139201 0.048
A_55_P1981674 0.079
A_55_P2290443 0.045
A_55_P2028350 0.075
A_55_P2067011 0.068
A_55_P1963384 0.050
A_55_P2082250 0.045
A_55_P1957294 0.049
A_55_P2279977 0.046
A_55_P2017100 0.112
A_55_P1995602 0.048
A_55_P2263762 0.063
A_55_P2341025 0.051
A_55_P2368366 0.227
A_55_P2061724 0.084
A_55_P2222377 0.049
A_55_P1960738 0.046

Total number of rows: 30629

Table truncated, full table size 591 Kbytes.




Supplementary file Size Download File type/resource
GSM2790259_GE_v2_16hr_1Gy_2.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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