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Sample GSM867885 Query DataSets for GSM867885
Status Public on Jan 01, 2013
Title No.2 vs No.7 Tamoxifen-treated wild type prostaspheres versus Tamoxifen-treated Sox9 prostaspheres
Sample type RNA
 
Channel 1
Source name No. 2 SOX9
Organism Mus musculus
Characteristics tissue: prospheres from UGE
treatment: Tamoxifen
genetic background: C57/Bl6J
genotype: SOX9 wild type
Treatment protocol After 6 days in matrigel plus 10–8 millimolar Dihydrotestosterone, prostaspheres were exposed to Tamoxifen (5 micromolar) or vehicle for 6 additional days. Prostaspheres were then snap frozen in liquid nitrogen.
Growth protocol C57/Bl6J, ERCre+/+Sox9flox/flox and ERCre+/+Sox9flox/+ urogenital sinus (UGS) were harvested at 16 days post conception. UGS were collected, digested, washed. Epithelial cells then were isolated, minced and incubated in collagenase (1mg/ml) and DNase (1mg/ml). Cells were washed, cultured overnight and isolated into single cells. Prostate epithelial cells were washed, cultured overnight, isolated into single cells, and passed in Matrigel to form prostaspheres.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from homogenized frozen tissue using the RNeasy system (Qiagen). RNA quality was assessed using a Bioanalyzer 2100 (Agilent Technologies)
Label Cy5
Label protocol 250 ng of total RNA input was reverse transcribed into by oligo dT primer incorporating a T7 promoter sequence, and labelled cRNA was obtained by T7 RNA polymerase transcription (Low RNA Input Fluorescent Linear Amplification Kit, Agilent Technologies). cRNA was purified using RNeasy mini kit (Qiagen).
 
Channel 2
Source name No.7 Ctrl
Organism Mus musculus
Characteristics tissue: prospheres from UGE
treatment: Tamoxifen
genetic background: C57/Bl6J
genotype: Sox9 null
Treatment protocol After 6 days in matrigel plus 10–8 millimolar Dihydrotestosterone, prostaspheres were exposed to Tamoxifen (5 micromolar) or vehicle for 6 additional days. Prostaspheres were then snap frozen in liquid nitrogen.
Growth protocol C57/Bl6J, ERCre+/+Sox9flox/flox and ERCre+/+Sox9flox/+ urogenital sinus (UGS) were harvested at 16 days post conception. UGS were collected, digested, washed. Epithelial cells then were isolated, minced and incubated in collagenase (1mg/ml) and DNase (1mg/ml). Cells were washed, cultured overnight and isolated into single cells. Prostate epithelial cells were washed, cultured overnight, isolated into single cells, and passed in Matrigel to form prostaspheres.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from homogenized frozen tissue using the RNeasy system (Qiagen). RNA quality was assessed using a Bioanalyzer 2100 (Agilent Technologies)
Label cy3
Label protocol 250 ng of total RNA input was reverse transcribed into by oligo dT primer incorporating a T7 promoter sequence, and labelled cRNA was obtained by T7 RNA polymerase transcription (Low RNA Input Fluorescent Linear Amplification Kit, Agilent Technologies). cRNA was purified using RNeasy mini kit (Qiagen).
 
 
Hybridization protocol Fragmentation was carried out by the Sidney Kimmel Comprehensive Cancer Center Microarray Core Facility by incubating at 60 degrees Celsius for 30 minutes and stopped by adding equal volume of 2x hybridization buffer (Agilent Technologies). Fragmented targets were added on Agilent Whole Mouse Genome G4122A Microarrays (Agilent Technologies). The microarrays were assembled into a hybridization chamber (Agilent Technologies) and hybridized at 60 degrees Celsius for 17 hours in a hybridization oven with rotation. Hybridized microarrays were washed and dried according to the Agilent microarray processing protocol.
Scan protocol Microarrays were scanned by the Sidney Kimmel Comprehensive Cancer Center Microarray Core Facility with the Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays with 100% PMT and 10 micometer resolutions. Data was extracted using Feature Extraction Software version 10.5.1.1 (Agilent Technologies).
Data processing Within-array dye effects were corrected by the 'loess' normalization method. No background subtraction was performed prior to normalization. Positive and negative microarray control features were not used to compute the 'loess' smoothing and were further excluded from subsequent analyses. Data pre-processing was performed using the R/Bioconductor package 'limma'.
 
Submission date Jan 30, 2012
Last update date Jan 01, 2013
Contact name Luigi Marchionni
E-mail(s) marchion@jhu.edu
Phone 410-502-8179
Organization name Johns Hopkins University
Department Oncology
Lab Cancer Biology Program
Street address 1550 Orleans St., CRB2, Room 1M52
City Baltimore
State/province MD
ZIP/Postal code 21231
Country USA
 
Platform ID GPL4134
Series (1)
GSE35419 Sox9 mediated differential gene expression was assessed in prostaspheres derived from urogenital sinus epithelial cells

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (M-value)

Data table
ID_REF VALUE
12 -0.266710484
13 -0.165504351
14 -0.423595611
15 -0.1335756
16 -0.787314884
18 -0.162488769
19 -0.38817286
20 -0.054741438
21 -0.317331186
22 -0.12193404
23 -0.181489524
24 -0.027808556
25 -0.091073084
26 -0.217748493
27 -0.003879636
28 -2.021966725
29 0.087429227
30 -0.347312377
31 -0.299004599
32 -0.400155515

Total number of rows: 43379

Table truncated, full table size 769 Kbytes.




Supplementary file Size Download File type/resource
GSM867885_jhu_251486824081_S01_GE2_105_Jan09_1_1_No.2_cy5_No.7_cy3.txt.gz 15.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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