|
| Status |
Public on May 01, 2011 |
| Title |
S_3_days_YFP_pos_2 |
| Sample type |
RNA |
| |
|
| Source name |
3 days YFP pos
|
| Organism |
Mus musculus |
| Characteristics |
strain: Foxl1-CRE; RosaYFP mouse
yfp expression: YFP positive
days of ddc treatment: 3
tissue: liver
cell type: non-parenchymal
|
| Treatment protocol |
Foxl1-Cre; RosaYFP mice were fed a DDC diet for 3, 7, and 14 days, and YFP+ and YFP- were isolated from total non-parenchymal cells that are negative for CD45. Total non-parenchymal cells from chow-fed mice were used as controls.
|
| Growth protocol |
Foxl1-CRE mice were crossed with Rosa26R FYP reporter mice. Offspring were 6 to 10 weeks old.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from liver samples and sorted cells using Trizol and RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
Amplified cDNA was prepared using the WT-Ovation Pico Amplification System (NuGEN Technologies). Amplified cDNA was directly labeled using the BioPrime Array CGH Genomic Labeling System with Cy3-labeled nucleotides (GE Amersham Biosciences).
|
| |
|
| Hybridization protocol |
Labeled samples were hybridized overnight to the Agilent 4X44 Whole Mouse Genome Array.
|
| Scan protocol |
Arrays were washed and then scanned with the model G2565B Agilent DNA microarray Scanner (Agilent Technologies).
|
| Data processing |
Median intensities of each element on the array were captured with Agilent Feature Extraction version 9.53 (Agilent Technologies). Quality control diagnostic plots were prepared for each array, and those failing to exhibit high-quality hybridizations were excluded from further analysis, resulting in the final dataset containing four biological replicates for each condition. The subsequent analysis was performed as previously (Rieck et al. 2009).
|
| |
|
| Submission date |
Apr 27, 2011 |
| Last update date |
May 01, 2011 |
| Contact name |
Jonathan Schug |
| E-mail(s) |
jschug@pennmedicine.upenn.edu
|
| Phone |
215 898 0773
|
| Organization name |
University of Pennsylvania
|
| Department |
School of Medicine
|
| Lab |
Next-Generation Sequencing Core
|
| Street address |
12-156 Smilow Ctr Trans Research
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104-5160 |
| Country |
USA |
| |
|
| Platform ID |
GPL4134 |
| Series (2) |
| GSE28890 |
Foxl1-Cre-marked Adult Hepatic Progenitors Have Clonogenic and Bi-Lineage Differentiation Potential - Time Course |
| GSE28892 |
Foxl1-Cre-marked Adult Hepatic Progenitors Have Clonogenic and Bi-Lineage Differentiation Potential |
|
