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Sample GSM12262 Query DataSets for GSM12262
Status Public on Mar 11, 2004
Title MeHg: PK11195 intervention at 4.5h
Sample type RNA
 
Channel 1
Source name 5.0 mg/kg MeHg + PK11195
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name MeHg treated prosencephalon
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Date : 3/29/2002
Original sample
Species : Mouse
Strain : CD-1 (outbred)
Genotype : wild-type
Stage : 9 d.p.c., Theiler stage 14
Tissue : forebrain & surrounding tissue
Treatments applied
Agent : methylmercury
Route : single i.p. injection
Dose : 5.0 mg/kg
Time : 4.5 hrs post-injection
Intervention : 4.0 mg/kg PK11195 co-administered
Risk: anticipated remediation to <10% malformations
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement : conventional microdissection
Sampling unit : 10-12 forebrains pooled from two litters
Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition : 56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix : 4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = methylmercury
Keywords = PK11195
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = SC862
 
Submission date Oct 23, 2003
Last update date May 28, 2005
Contact name Thomas B Knudsen
E-mail(s) singh.amarv@epamail.epa.gov
Phone 502-852-4128
Fax 502-852-4702
URL http://systemsanalysis.louisville.edu/
Organization name University of Louisville
Department Birth Defects Center
Lab Systems Analysis Laboratory
Street address 501 S Preston St
City Louisville
State/province KY
ZIP/Postal code 40202
Country USA
 
Platform ID GPL560
Series (2)
GSE1072 Comparison of Bzrp ligands
GSE1077 MeHg intervention with PK11195

Data table header descriptions
ID_REF
VALUE Normalized log2(Test/Reference)
SC862_cy5 Test
SC862_cy3 Reference

Data table
ID_REF VALUE SC862_cy5 SC862_cy3
1 -0.394 682.00 1564.50
2 -0.018 175.50 410.50
3 -0.129 344.50 793.50
4 0.378 385.50 725.00
5 -0.107 2249.00 6046.00
6 0.892 -40.00 177.00
7 0.454 658.00 1082.00
8 0.334 585.50 1154.50
9 -0.969 411.50 977.50
10 0.309 627.50 1461.50
11 -0.468 1947.50 4766.50
12 -0.163 1495.50 4276.50
13 -0.618 14151.50 37944.00
14 0.510 2255.50 4167.00
15 0.283 -50.00 -66.50
16 -0.290 299.00 833.00
17 -0.653 335.00 914.50
18 0.054 568.00 1109.50
19 -0.253 125.00 478.50
20 -0.352 1608.00 4365.50

Total number of rows: 2382

Table truncated, full table size 61 Kbytes.




Supplementary data files not provided

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