|
| Status |
Public on Apr 14, 2015 |
| Title |
Non-irradiated/vehicle Sox9-EGFP High rep 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Sorted intestinal epithelial cells expressing High 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: High
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 1/7; FACS-isolated intestinal epithelial cells expressing High 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 22
|
| 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) |
[email protected]
|
| 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 |
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