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Sample GSM571025 Query DataSets for GSM571025
Status Public on Jul 29, 2010
Title aERKO HPTE 24hr vs V
Sample type RNA
 
Channel 1
Source name aERKO uterus sesame oil HPTE 24h
Organism Mus musculus
Characteristics esr1 genotype: aERKO (Esr1 null)
strain: C57Bl/6J
age: adult (10+ weeks)
gender: ovariectomized female
Treatment protocol ovariectomized mice were allowed to rest for 10-14 days, then injected with saline or 250ng estradiol, 100 ul sesame oil or 750 ug BPA or HPTE in 100 ul oil ip. Uterine tissue was collected 2 or 24 hours after injection and frozen in liquid nitrogen
Extracted molecule total RNA
Extraction protocol pools of 3 frozen uteri were pulverized and homogenized in Trizol (Invitrogen 5- 100 mg tissue/ml Trizol, minimum 800 ul) . Extraction proceeded as descibed in manufacturer's protocol. Following resuspension of RNA pellet, a second preciptation was done with NaAcetate and ethanol. This pellet was then resuspended in depc treated water and cleaned up using the Qiagen RNeasy kit clean up protocol. RNA concentration and A260/280 was checked and quality was evaluated by formaldehyde gel.
Label Cy3
Label protocol Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500ng of total RNA, Cy3 labeled cRNA and Cy5 labeled cRNA were produced according to manufacturer’s protocol.
 
Channel 2
Source name aERKO uterus sesame oil V
Organism Mus musculus
Characteristics esr1 genotype: aERKO (Esr1 null)
strain: C57Bl/6J
age: adult (10+ weeks)
gender: ovariectomized female
Treatment protocol ovariectomized mice were allowed to rest for 10-14 days, then injected with saline or 250ng estradiol, 100 ul sesame oil or 750 ug BPA or HPTE in 100 ul oil ip. Uterine tissue was collected 2 or 24 hours after injection and frozen in liquid nitrogen
Extracted molecule total RNA
Extraction protocol pools of 3 frozen uteri were pulverized and homogenized in Trizol (Invitrogen 5- 100 mg tissue/ml Trizol, minimum 800 ul) . Extraction proceeded as descibed in manufacturer's protocol. Following resuspension of RNA pellet, a second preciptation was done with NaAcetate and ethanol. This pellet was then resuspended in depc treated water and cleaned up using the Qiagen RNeasy kit clean up protocol. RNA concentration and A260/280 was checked and quality was evaluated by formaldehyde gel.
Label Cy5
Label protocol Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500ng of total RNA, Cy3 labeled cRNA and Cy5 labeled cRNA were produced according to manufacturer’s protocol.
 
 
Hybridization protocol For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.
Scan protocol Slides were washed as indicated in the Agilent 60-mer oligo microarray processing protocol and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters.
Description US22502532_251486813439_S01_H.tif
US22502532_251486813439__S01_L.tif
gene expression in aERKO ovariectomized oil vehicle vs HPTE 24h treated uterus
Data processing Data was obtained using the Agilent Feature Extraction software (v9.1), using defaults for all parameters. The default setting for the protocol we used is polynomial data fit.
 
Submission date Jul 27, 2010
Last update date Jul 29, 2010
Contact name NIEHS Microarray Core
E-mail(s) microarray@niehs.nih.gov, liuliw@niehs.nih.gov
Organization name NIEHS
Department DIR
Lab Microarray Core
Street address 111 T.W. Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL4134
Series (1)
GSE18168 Uterine gene profiles from WT, KIKO (DNA-binding deficient ERα) and aERKO mice treated with estradiol or xenoestrogens

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3
INV_VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE INV_VALUE
1 0.106112 -1.061115768e-001
2 0.000000000e+000 0.000000000e+000
3 0.000000000e+000 0.000000000e+000
4 0.000000000e+000 0.000000000e+000
5 0.000000000e+000 0.000000000e+000
6 0.000000000e+000 0.000000000e+000
7 0.000000000e+000 0.000000000e+000
8 0.000000000e+000 0.000000000e+000
9 0.000000000e+000 0.000000000e+000
10 0.000000000e+000 0.000000000e+000
11 0.000000000e+000 0.000000000e+000
12 0.000000000e+000 0.000000000e+000
13 0.138425 -1.384251573e-001
14 -0.0366668 3.666681329e-002
15 -0.082202 8.220201321e-002
16 0.105843 -1.058433717e-001
18 -0.190441 1.904414083e-001
19 0.293484 -2.934838843e-001
20 -0.0375463 3.754625016e-002
21 0.0462533 -4.625334283e-002

Total number of rows: 45018

Table truncated, full table size 1511 Kbytes.




Supplementary file Size Download File type/resource
GSM571025_US22502532_251486813439_S01_GE2-v5_91_0806_1_2.txt.gz 14.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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