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Sample GSM624918 Query DataSets for GSM624918
Status Public on Dec 01, 2011
Title prostate_VP_low_fat_rep1
Sample type RNA
 
Source name Ventral Prostate of mouse fed with a low fat and no cholesterol diet
Organism Mus musculus
Characteristics strain: SCID
gender: male
tissue: prostate
prostate region: VP
diet: low fat and no cholesterol
Treatment protocol After 6 weeks, the prostates of the mice were separately extracted as Ventral Prostate(VP), Dorsal Lateral Prostate (DLP), and Anterior Prostate (AP).
Growth protocol In total, 18 SCID male mice were used in the study, one group of mice was fed a high fat and high cholesterol (HFHC) diet, and another group of 9 mice were fed a low fat and no cholesterol diet (LFNC).
Extracted molecule total RNA
Extraction protocol The RNAs were extracted using a Qiagen RNEasy tissue extraction kit (Qiagen Inc., Valencia, California).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Microarray hybridization was performed by following general Affymetrix protocol at Dana-Farber Cancer Institute microarray core facility.
Scan protocol Scanning of microarrays were performed by following general Affymetrix protocol at Dana-Farber Cancer Institute microarray core facility.
Description Gene expression data from Ventral Prostate of mouse fed with a low fat and no cholesterol diet
Data processing Data normalization and summarization of expression values for each probe were calculated using gcRMA method. Quantile normalization of the data was performed with gcrma R/Bioconductor package v2.11.
 
Submission date Nov 17, 2010
Last update date Dec 01, 2011
Contact name Taek-Kyun Kim
URL http://sbm.postech.ac.kr
Organization name POSTECH
Department Interdisciplinary Bioscience and Bioengineering
Lab Systems Biology and Medicine Laboratory
Street address San 31, Hyoja-dong, Nam-gu
City Pohang
State/province Gyeongbuk
ZIP/Postal code 790-784
Country South Korea
 
Platform ID GPL8321
Series (2)
GSE25461 Gene expression of three prostate lobes, ventral prostate (VP), dorsal lateral prostate (DLP), and anterior prostate (AP), by cholesterol diet
GSE25500 The Response of the Prostate to Changes in Circulating Cholesterol: Activating Transcription Factor 3 (ATF3) as a Cholesterol Sensor

Data table header descriptions
ID_REF
VALUE quantile normalized signal intensity

Data table
ID_REF VALUE
1415670_at 8.299289092
1415671_at 8.457235251
1415672_at 6.342365942
1415673_at 6.077608885
1415674_a_at 7.342335943
1415675_at 7.945361703
1415676_a_at 9.229556525
1415677_at 5.764416378
1415678_at 6.651538695
1415679_at 9.317205758
1415680_at 7.279250435
1415681_at 8.4563684
1415682_at 5.27346577
1415683_at 8.302855316
1415684_at 5.730747401
1415685_at 5.843251086
1415686_at 7.481218844
1415687_a_at 10.41991743
1415688_at 8.207055576
1415689_s_at 4.328358381

Total number of rows: 22690

Table truncated, full table size 521 Kbytes.




Supplementary file Size Download File type/resource
GSM624918.CEL.gz 1.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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