|
| Status |
Public on Dec 25, 2018 |
| Title |
preproB_EnhDel_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
preproB Cebpa enhancer-deleted replicate 2
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: bone marrow
gender: male
age: 24 wks
genotype/variation: without the +37 kb Cebpa enhancer
|
| Treatment protocol |
pIpC 300 mg s.q. every other day for 3 doses, then wait 5 wks to isolate marrow and then preproB cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cells were sorted into Trizol, chloroform extracted, and upper phase added to equal volume ethanol and then applied to RNA Clean and Concentrator-5 (Zymo Research) columns and Eluted with 15 ml water to isolate RNA.
|
| Label |
Cy3
|
| Label protocol |
Sample amplification and labeling were carried out by using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The labeled cRNA were purified using RNeasy mini kit (Qiagen).
|
| |
|
| Hybridization protocol |
0.825 ug of each Cy3-labeled sample was used for hybridization at 65ºC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays are washed and dried according to Agilent microarray processing protocol in a walk-in ozone-controlled enclosure.
|
| Scan protocol |
Microarrays were scanned using an Agilent G2565A Scanner controlled by Agilent Scan Control 7.0 software. Data were extracted with Agilent Feature Extraction 9.5.3.1 software.
|
| Description |
Gene expression, enhancer deletion
|
| Data processing |
Agilent FE processed signal intensities were imported into GeneSpring GX 10 (Agilent Technologies). Normalization was done by setting intensity thresheld to 5 and log2 transformation.
|
| |
|
| Submission date |
Feb 01, 2018 |
| Last update date |
Dec 25, 2018 |
| Contact name |
Alan D Friedman |
| E-mail(s) |
afriedm2@jhmi.edu
|
| Phone |
410-955-2095
|
| Organization name |
Johns Hopkins University
|
| Department |
Oncology
|
| Lab |
CRB I, Rm. 253
|
| Street address |
1650 Orleans St.
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21231 |
| Country |
USA |
| |
|
| Platform ID |
GPL10333 |
| Series (1) |
| GSE110029 |
RNA Expression (log2) in preproB Cells from Two Cebpa +37 kb Enhancer(f/f) or Cebpa +37 kb Enhancer(f/f);Mx1-Cre Mice Exposed to pIpC 5 Weeks Earlier |
|
