|
| Status |
Public on Sep 22, 2006 |
| Title |
4C_beta-major-fetal_brain-2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
genomic DNA digested with HindIII and NlaIII
|
| Organism |
Mus musculus |
| Characteristics |
genomic DNA C57BL/6
|
| Extracted molecule |
genomic DNA |
| Label |
Cy3
|
| |
|
| Channel 2 |
| Source name |
4C sample obtained from E14.5 brain, digested with HindIII and NlaIII
|
| Organism |
Mus musculus |
| Characteristics |
4C sample containing DNA amplified by inverse PCR using primers specific for a HindIII restriction fragment encompassing the beta-major gene (Hbb-b1).
|
| Extracted molecule |
genomic DNA |
| Label |
Cy5
|
| |
|
| |
| Description |
Unprocessed (not normalized) hybridization ratios were used for analysis. These ratios showed clusters of 20-50 positive 4C-signals along the chromosome template. To define the clusters, a running mean or running median was applied, using a window size of 29 probes (on average 60 kb). Obtained values were compared to the running mean/median performed across randomized data. This was done for each array separately. Consequently, all measurements were appreciated relative to the amplitude and noise of that specific array. The False Discovery Rate (FDR), defined as (no. false positives) / (no. of false positives + no. of true positives), was determined as follows: (number of positives in the randomised set) / (number of positives in the data). The threshold level was determined using a top down approach to establish the minimal value for which: FDR<0.05.
|
| Data processing |
The signal ratio 4C-sample/genomic DNA was calculated for each probe.
|
| |
|
| Submission date |
Sep 21, 2006 |
| Last update date |
Sep 21, 2006 |
| Contact name |
Wouter de Laat |
| E-mail(s) |
w.delaat@erasmusmc.nl
|
| Phone |
31-10-4087164
|
| Fax |
31-10-4089468
|
| URL |
http://www2.eur.nl/fgg/ch1/delaat.html
|
| Organization name |
Erasmus MC
|
| Department |
Cell Biology
|
| Street address |
Dr. Molewaterplein 50
|
| City |
Rotterdam |
| ZIP/Postal code |
3015 GE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL4345 |
| Series (1) |
| GSE5891 |
Nuclear organization of active and inactive chromatin domains revealed by 4C technology |
|
