|
| Status |
Public on Jan 18, 2009 |
| Title |
Undifferentiated ES |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Chromatin immunoprecipitated DNA from Undifferentiated ES cells using H3K9Me2 antibody
|
| Organism |
Mus musculus |
| Characteristics |
Undifferentiated ES
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Performed by NimbleGen using standard protocol
|
| Label |
Cy5
|
| Label protocol |
Performed by NimbleGen using standard protocol
|
| |
|
| Channel 2 |
| Source name |
Input DNA
|
| Organism |
Mus musculus |
| Characteristics |
Undifferentiated ES
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Performed by NimbleGen using standard protocol
|
| Label |
Cy3
|
| Label protocol |
Performed by NimbleGen using standard protocol
|
| |
|
| |
| Hybridization protocol |
Performed by NimbleGen using standard protocol
|
| Scan protocol |
Performed by NimbleGen using standard protocol
|
| Description |
Undifferentiated ES
|
| 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 |
Oct 24, 2008 |
| Last update date |
Jan 13, 2009 |
| Contact name |
Andrew P. 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 (1) |
| GSE13445 |
Large organized chromatin K9-modifications (LOCKs) distinguish differentiated from embryonic stem cells |
|
