|
| Status |
Public on Apr 27, 2015 |
| Title |
ncor_2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
ncor chIP, KH2 cells, 2 hrs RA
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse Embryonic Stem Cells (KH2)
timepoint: 2 hrs after RA
chip antibody: ncor
chip antibody vendor: Abcam
chip antibody catalog: Ab24552
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
37 degrees C for 11 min. Crosslinking was stopped by 1mL 1.25 M glycine to each 10 mL and by incubating at room temperature for 5 min. Cells were sonicated for 25 min in bioruptor at high setting and 30 sec on-off cycle. Input DNA and IP DNA in the amount of 10ng were amplified according to the Agilent Genomic DNA Labeling Kit PLUS (Agilent, 5188-5309, Agilent publication number G4481-90010).
|
| Label |
Cy5
|
| Label protocol |
Extracts were labeled according to Agilent Genomic DNA Labeling Kit PLUS (Agilent, 5188-5309, Agilent publication number G4481-90010).
|
| |
|
| Channel 2 |
| Source name |
ncor chIP, KH2 cells, 2 hrs RA
|
| Organism |
Mus musculus |
| Characteristics |
sample type: input
cell type: KH2 cells
timepoint: 2 hrs after RA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
37 degrees C for 11 min. Crosslinking was stopped by 1mL 1.25 M glycine to each 10 mL and by incubating at room temperature for 5 min. Cells were sonicated for 25 min in bioruptor at high setting and 30 sec on-off cycle. Input DNA and IP DNA in the amount of 10ng were amplified according to the Agilent Genomic DNA Labeling Kit PLUS (Agilent, 5188-5309, Agilent publication number G4481-90010).
|
| Label |
Cy3
|
| Label protocol |
Extracts were labeled according to Agilent Genomic DNA Labeling Kit PLUS (Agilent, 5188-5309, Agilent publication number G4481-90010).
|
| |
|
| |
| Hybridization protocol |
Arrays were hybridized with a mixture of 4µg Cy3 labeled DNA and 4µg Cy5 labeled DNA probes. Hybridizations were performed at 650C for 24 hours under standard conditions (45 mg/mL Human Cot-1 DNA, 1X Agilent blocking agent, and 1X Agilent hybridization buffer) and slides were washed successively with Agilent ChIP wash buffer 1, at room temperature and then Agilent ChIP wash buffer 2, at 31C, prior to scanning.
|
| Scan protocol |
Microarray images were acquired with an Agilent High-Resolution DNA Microarray Scanner (G2505C). For image analysis Agilent Feature Extraction software (Version 10.5.1.1) was used.
|
| Data processing |
Agilent tiling arrays were hybridized in a two-color configuration and data was read into R (2.11.1). Data was analyzed using the limma (3.4.3) package. Data was normalized within arrays using loess normalization.
|
| |
|
| Submission date |
Sep 19, 2014 |
| Last update date |
Apr 27, 2015 |
| Contact name |
Madelaine Gogol |
| Organization name |
Stowers Institute
|
| Department |
Computational Biology Core
|
| Street address |
1000 E. 50th Street
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL19237 |
| Series (2) |
| GSE61584 |
Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters (ChIP-chip) |
| GSE61590 |
Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters |
|
