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Sample GSM1050491 Query DataSets for GSM1050491
Status Public on Apr 14, 2015
Title Non-irradiated/vehicle Sox9-EGFP Sublow rep 4
Sample type RNA
 
Channel 1
Source name Sorted intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene
Organism Mus musculus
Characteristics strain: CD-1
developmental stage: adult
gender: male
tissue: small intestine - jejunum
mouse model: Sox9-EGFP BAC transgenic mice
level of expression of the sox9-egfp reporter gene: Sublow
treatment: non-irradiated - vehicle (control)
Treatment protocol Sox9-EGFP transgenic mice were given a single dose of 14Gy abdominal irradiation using an XRAD320 (Precision X-Ray, East Haven, CT - Filter: 2mm, Al; 47cm ; 320kV/s, 10mA; 2.8Gy/min). Immediately following radiation, mice were implanted mini pumps (Alzet, Cupertino, CA, model 1007D, subcutaneously) filled with either vehicle (NaCl 0.9%) or IGF1 (Genentech, 10mg/ml). Mice were euthanized 5 days after radiation/mini-pump implantation, jejunum was collected and processed for single cell dissociation. Cells expressing either Negative, Sublow, Low or HIgh levels of the Sox9-EGFP transgene were isolated by FACS. Non-irradiated control mice were included in the same run of FACS and gating was defined using EGFP intensity profile of the non-irradiated controls.
Growth protocol Sox9-EGFP BAC transgenic mice used between 6-10 weeks old
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Qiagen Rneasy mini kit (Qiagen, Venlo, The Netherlands) following manufacturer's instructions
Label Cy5
Label protocol 0.1-1µg ot total RNA was amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit, Two-Color (5190-2306, Santa Clara, CA) - Cy5 for samples and Cy3 for reference
 
Channel 2
Source name Pool of non-sorted intestinal epithelial cells from non-irradiated mice
Organism Mus musculus
Characteristics strain: CD-1
developmental stage: adult
gender: male
tissue: small intestine - jejunum
mouse model: Sox9-EGFP BAC transgenic mice
level of expression of the sox9-egfp reporter gene: non-applicable (unsorted)
treatment: non-irradiated - vehicle (control)
Treatment protocol Sox9-EGFP transgenic mice were given a single dose of 14Gy abdominal irradiation using an XRAD320 (Precision X-Ray, East Haven, CT - Filter: 2mm, Al; 47cm ; 320kV/s, 10mA; 2.8Gy/min). Immediately following radiation, mice were implanted mini pumps (Alzet, Cupertino, CA, model 1007D, subcutaneously) filled with either vehicle (NaCl 0.9%) or IGF1 (Genentech, 10mg/ml). Mice were euthanized 5 days after radiation/mini-pump implantation, jejunum was collected and processed for single cell dissociation. Cells expressing either Negative, Sublow, Low or HIgh levels of the Sox9-EGFP transgene were isolated by FACS. Non-irradiated control mice were included in the same run of FACS and gating was defined using EGFP intensity profile of the non-irradiated controls.
Growth protocol Sox9-EGFP BAC transgenic mice used between 6-10 weeks old
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Qiagen Rneasy mini kit (Qiagen, Venlo, The Netherlands) following manufacturer's instructions
Label Cy3
Label protocol 0.1-1µg ot total RNA was amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit, Two-Color (5190-2306, Santa Clara, CA) - Cy5 for samples and Cy3 for reference
 
 
Hybridization protocol Hybridization was performed using the Agilent Gene Expression Hybridization Kit (5188-5242, Santa Clara, CA) and the Agilent Microarray Hybridization Chamber Kit (G2534A, Santa Clara, CA)
Scan protocol Slides were scanned using Agilent Microarray Scanner and Agilent Scan Control software (Santa Clara, CA)
Description Biological replicate 4/7; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 11
Data processing Scanned images were analyzed, data were processed and LogRatio analysis was perfomed using Agilent Feature Extraction Software version 10.7.3.1 (Santa Clara, CA)
 
Submission date Dec 10, 2012
Last update date Apr 14, 2015
Contact name P. Kay Lund
E-mail(s) laurianne_van_landeghem@med.unc.edu
Phone 919 966 1490
Fax 919 966 6927
Organization name UNC at Chapel Hill
Department Cell and Molecular Physiology
Lab Lund
Street address 6336 MBRB CB 7545 111 Mason Farm Road
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7545
Country USA
 
Platform ID GPL10333
Series (1)
GSE42817 Characterization of IGF1 effects on the transcriptome of normal and irradiated Sox9-EGFP cell populations

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

Data table
ID_REF VALUE
1 -3.849401789e-001
2 0.000000000e+000
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 0.000000000e+000
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 0.000000000e+000
12 -7.765151377e-001
13 -1.292062541e-001
14 -7.503238429e-001
15 -2.219357588e-001
16 -4.052155434e-002
17 -3.186269847e-001
18 1.739503812e-001
19 0.000000000e+000
20 1.342682307e-001

Total number of rows: 44397

Table truncated, full table size 1002 Kbytes.




Supplementary file Size Download File type/resource
GSM1050491_US82800149_252665510739_S01_GE2_105_Dec08_1_1.txt.gz 15.5 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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