|
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
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|
|
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.
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|
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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 |
|