|
| Status |
Public on Jul 03, 2011 |
| Title |
H3K9me2 36-hour TGFb, array 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
ChIP against H3K9me2
|
| Organism |
Mus musculus |
| Characteristics |
cell type: AML12
antibody: H3K9me2
vendor: Abcam
cat#: ab1220
lot#: 764743
sample type: input DNA
|
| Treatment protocol |
TGF-β treatment for 36hrs
|
| Growth protocol |
Confluent cultures serum starved for 48hrs before treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Performed according to standard NimbleGen protocol
|
| Label |
Cy5
|
| Label protocol |
Labels with Cy3 and Cy5 were performed according to standard NimbleGen protocol
|
| |
|
| Channel 2 |
| Source name |
Genomic DNA
|
| Organism |
Mus musculus |
| Characteristics |
antibody: none
|
| Treatment protocol |
TGF-β treatment for 36hrs
|
| Growth protocol |
Confluent cultures serum starved for 48hrs before treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Performed according to standard NimbleGen protocol
|
| Label |
Cy3
|
| Label protocol |
Labels with Cy3 and Cy5 were performed according to standard NimbleGen protocol
|
| |
|
| |
| Hybridization protocol |
Performed according to standard NimbleGen protocol
|
| Scan protocol |
Performed according to standard NimbleGen protocol with NimbleGen software (Signalmap)
|
| Data processing |
Briefly, we first quantile normalized Cy3 (Input) intensities from all arrays to a common target. We used a smoothing procedure to improve the signal to noise ratio of the M (log2 ratio Cy5/Cy3) values and fitted a function of M values to the chromosomal location using loess. We then picked the genomic regions with the lowest 20% fitted values as the reference region. The Cy5 intensities in the reference regions should have similar distributions in each sample. We therefore quantile normalized them to the same distribution target. The quantile procedure was used to construct a function to map pre-normalization Cy5 intensities to post-normalization Cy5 intensities. This map was then applied to all the Cy5 intensities. This procedure made the M values comparable from array to array.
|
| |
|
| Submission date |
Mar 31, 2011 |
| Last update date |
Jul 03, 2011 |
| Contact name |
Andrew Feinberg |
| E-mail(s) |
afeinberg@jhu.edu
|
| Organization name |
Johns Hopkins University
|
| Department |
Center for Epigenetics and Department of Medicine
|
| Street address |
855 N. Wolfe Street
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21212 |
| Country |
USA |
| |
|
| Platform ID |
GPL7524 |
| Series (2) |
| GSE28291 |
Genome-scale epigenetic reprogramming during epithelial to mesenchymal transition |
| GSE28581 |
Epigenomic reprogramming during epithelial to mesenchymal transition |
|
