|
| Status |
Public on Apr 20, 2007 |
| Title |
US22502648_251357810008_S01_44k_CGH |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Neuralized EBs ChIP Biological Rep#2 Technical Rep#3
|
| Organism |
Mus musculus |
| Characteristics |
Neuralized Embryoid bodies treated with 500nM retinoic acid and 1µm of HH Agonist (HH-Ag)
|
| Biomaterial provider |
Steve Vokes
|
| Treatment protocol |
Neuralized Embryoid bodies treated with 500nM retinoic acid and 1µm of HH Agonist (HH-Ag)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin prep and shearing, crosslinks reversed, LMPCR amplification
|
| Label |
Cy3
|
| Label protocol |
2 µg of amplified DNA was labeled with Cy3-dUTP (Perkin Elmer) using the Bioprime Array CGH kit (Invitrogen) per Agilent’s recommended protocol. 5 µg of amplified material was used for each channel during hybridization
|
| |
|
| Channel 2 |
| Source name |
Neuralized EBs Input Biological Rep#2 Technical Rep#3
|
| Organism |
Mus musculus |
| Characteristics |
Neuralized Embryoid bodies treated with 500nM retinoic acid and 1µm of HH Agonist (HH-Ag)
|
| Biomaterial provider |
Steve Vokes
|
| Treatment protocol |
Neuralized Embryoid bodies treated with 500nM retinoic acid and 1µm of HH Agonist (HH-Ag)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin prep and shearing, crosslinks reversed, LMPCR amplification
|
| Label |
Cy5
|
| Label protocol |
2 µg of amplified DNA was labeled with Cy5-dUTP (Perkin Elmer) using the Bioprime Array CGH kit (Invitrogen) per Agilent’s recommended protocol. 5 µg of amplified material was used for each channel during hybridization
|
| |
|
| |
| Hybridization protocol |
Arrays were hybridized by competitive hybridization using 5µg of labeled material per channel using the Oligo CGH hybridization kit (Agilent Technologies). The hybridizations were done in Agilent SureHyb hybridization chambers and in an Agilent rotating hyb oven at a speed of 10rpm for 72 hours at 65º C. Samples were washed sequentially for 5 minutes at room temperature using Oligo aCGH wash buffer 1, 1 minute at 37º C using Oligo aCGH wash buffer 2, 1 minute in acetonitrile at room temperature and 30 seconds in stabilization and drying solution (all from Agilent technologies).
|
| Scan protocol |
Finished arrays were scanned using an Agilent scanner. The settings were 10µm resolution and the PMT setting of both channels was at 100. Array images were extracted using Agilent’s Feature Extraction Software (version 8.5.1.1) using the standard CGH protocol included with the software. The settings included spatial detrending of the extracted array data and a linear median normalization
|
| Description |
This is biological replicate #2 technical replicate #3. All control spots were removed from this dataset because they have redundant names. If needed, they are present in the attached original dataset.
|
| Data processing |
The Value column is the Log Ratio of the two channels
|
| |
|
| Submission date |
Aug 31, 2006 |
| Last update date |
Jan 29, 2022 |
| Contact name |
Steven A. Vokes |
| E-mail(s) |
svokes@austin.utexas.edu
|
| Organization name |
University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Street address |
2500 Speedway, STOP A5000
|
| City |
Austin |
| State/province |
Texas |
| ZIP/Postal code |
78757 |
| Country |
USA |
| |
|
| Platform ID |
GPL4245 |
| Series (1) |
| GSE5683 |
Identification of Gli-Act targets in the mouse ventral neural tube by ChIP |
|
