|
| Status |
Public on Aug 21, 2011 |
| Title |
UL3 Bare, repeat 1 |
| Sample type |
genomic |
| |
|
| Source name |
Mononucleosomal MNase fragments from UL3 cells, bare DNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: UL3 (U20S w/ GR and MMTV-luc)
|
| Treatment protocol |
no treatment (control)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was extracted from cells using NP40 lysis, digested with micrococcal nuclease (MNase) to ~70% mononucleosomes and mononucleosomes isolated by PAGE and elution
|
| Label |
Cy3
|
| Label protocol |
1 to 4 micrograms of each mononcleosomal sample were labeled with Cy3 or Cy5 by Nimblegen services, according to their standard procedures
|
| |
|
| Hybridization protocol |
Hybridization was performed by Nimblegen accoring to standard procedures
|
| Scan protocol |
Scanning was performed by Nimblegen using Nimblescan version 2.4.27
|
| Description |
MNase digested bare DNA from UL3 cells (sample 1)
|
| Data processing |
For each position, two forward and two reverse oliogs were tiled on the array. Data for each set of oligos (nucleosomal & bare) were normalized to 1.0, and the ratio of nucl/(average bare 1 & bare2) determined. The median nucl/bare values for all 4 oligos were then quantile normalized for comparisons between conditions. The data was then locally smoothed by a combination of exponential smoothing of oligos within +/-40 bp (*0.5^(BP/10)) and by down-weighting positions where the deviation from the median value for F1,F2,R1 & R2 oligos was greater than average (*0.5^(deviation/avg_deviation)). Data processing was performed using custom PERL programs.
|
| |
|
| Submission date |
Nov 11, 2010 |
| Last update date |
Aug 21, 2011 |
| Contact name |
Gavin R. Schnitzler |
| E-mail(s) |
gavin.schnitzler@gmail.com
|
| Phone |
6086950428
|
| Organization name |
Tufts Medical Center
|
| Department |
Molecular Cardiology Research Institute
|
| Lab |
c/o Navin Kapur
|
| Street address |
800 Washington St. Box 80
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02111 |
| Country |
USA |
| |
|
| Platform ID |
GPL11196 |
| Series (1) |
| GSE25281 |
Nucleosome mapping data from GR and cell-cycle regulated genes in human cell lines |
|
