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Sample GSM444731 Query DataSets for GSM444731
Status Public on Aug 06, 2010
Title 1st 120 hrs monosomes
Sample type other
 
Channel 1
Source name Monosomal RNA extracted from cardiac tissue treated with 10ml/kg saline
Organism Mus musculus
Characteristics gender: Male
strain: C576B/AJ
age: 8 weeks
tissue: Heart
Treatment protocol Mice randomly assigned to control or treatment group and treated with 10ml/kg saline (control) or 15mg/kg doxorubicin in 10ml/kg(treatment) as sacrificed at 0.5, 1, 2, 12, 24, 120 hours following dosing, hearts quickly removed and snap frozen in liquid nitrogen
Growth protocol Mice housed with free assess to food and water, with a 12 hour light dark cycle
Extracted molecule other
Extraction protocol Cardiac tissue lysated and subjected to centrifugation on a 0-65% sucrose gradient allowing separation of RNA species, gradients fractionated into 1ml fractions directly into Trizol, RNA extracted according to the manufactures instructions. Equal volumes of polysome or monosome fractions combined. Control monosome and treated monosome were assayed on one microarray slide and control polysome and treated polysomes assayed on another microarray
Label Alexa 555
Label protocol Upto 10µg monosome or polysome RNA were primed with 1µl of 8µg/µl oligo dT25N2 at 70 oC for 10 minutes, then reverse transcribed at 50oC for 2 hours in the presence of 1µl Superscript III (Invitrogen) and 100µM each dATP, dTTP, dGTP with 25 µM dCTP and 25µM cy-3 or cy-5
 
Channel 2
Source name Monosomal RNA extracted from cardiac tissue treated with 15mg/kg doxorubicin in 10ml/kg saline
Organism Mus musculus
Characteristics gender: Male
strain: C576B/AJ
age: 8 weeks
tissue: Heart
Treatment protocol Mice randomly assigned to control or treatment group and treated with 10ml/kg saline (control) or 15mg/kg doxorubicin in 10ml/kg(treatment) as sacrificed at 0.5, 1, 2, 12, 24, 120 hours following dosing, hearts quickly removed and snap frozen in liquid nitrogen
Growth protocol Mice housed with free assess to food and water, with a 12 hour light dark cycle
Extracted molecule other
Extraction protocol Cardiac tissue lysated and subjected to centrifugation on a 0-65% sucrose gradient allowing separation of RNA species, gradients fractionated into 1ml fractions directly into Trizol, RNA extracted according to the manufactures instructions. Equal volumes of polysome or monosome fractions combined. Control monosome and treated monosome were assayed on one microarray slide and control polysome and treated polysomes assayed on another microarray
Label Alexa 647
Label protocol Upto 10µg monosome or polysome RNA were primed with 1µl of 8µg/µl oligo dT25N2 at 70 oC for 10 minutes, then reverse transcribed at 50oC for 2 hours in the presence of 1µl Superscript III (Invitrogen) and 100µM each dATP, dTTP, dGTP with 25 µM dCTP and 25µM cy-3 or cy-5
 
 
Hybridization protocol 4µg tRNA and 2x enhanced hybridization buffer (Genesiphere) were added, samples heated to 95oC for 2 minutes then 42oC for 30 minutes. Samples applied to microarrays enclosed in a Genetix humidified chamber. After hybridization overnight, slides were washed sequential.
Scan protocol Scanned on a Axon 4200A scanner
Images were quantified using Genepix 6.0 software
Description Samples normalized and A and B condensed into 1 file
none
Data processing LOWESS normalized, log2 of processed red signal / green signal, A and B files combined, the Log2 for the monosome arrays for each gene was subtracted from that of the polysome array, the resultant Log2 represents differential translation. These data are present on the Series record.
 
Submission date Aug 26, 2009
Last update date May 27, 2010
Contact name Amy Pointon
Organization name MRC Toxicology Unit
Department Systems Toxicology Group
Street address Lancaster Road
City Leicester
ZIP/Postal code LE1 9NH
Country United Kingdom
 
Platform ID GPL9106
Series (2)
GSE17823 Mouse cardiac tissue, polysomes and monosomes: Vehicle treated control vs. 15mg/kg doxorubicin
GSE18459 Mouse cardiac tissues treated with doxorubicin and DMNQ

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (red/green)

Data table
ID_REF VALUE
EMPTY
mCA000101 -0.136679
mCA000111 -0.219227
mCA000163 -0.126758
mCA000221 -0.223783
mCA000230 -0.675046
mCA000240 -0.093893
mCA000295 -0.177061
mCA000303
mCA000312 -2.45542
mCA000356 -0.445325
mCA000366 0.0832015
mCA000438
mCA000439
mCA000442
mCA000452 -1.05539
mCA000455
mCA000460
mCA000474 0.212145
mCA000483

Total number of rows: 38468

Table truncated, full table size 460 Kbytes.




Supplementary file Size Download File type/resource
GSM444731_1st_120_hrs_mono_A.gpr.gz 2.0 Mb (ftp)(http) GPR
GSM444731_1st_120_hrs_mono_B.gpr.gz 2.0 Mb (ftp)(http) GPR
Processed data included within Sample table
Processed data are available on Series record

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