|
| Status |
Public on Dec 08, 2009 |
| Title |
600mM_salt_fraction_2_(SOH39) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
H3.3 DNA salt 600mM cut
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
age: embryos
strain: N2 (Bristol)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nucleosomes were obtained using extraction of intact MNase-digested nuclei with 600mM NaCl. 600mM salt soluble fraction compared to MNAase treated starting material. Detailed protocol at http://nettie.fhcrc.org/modencode/protocols/Worm_Protocol.doc
|
| Label |
Cy3
|
| Label protocol |
Standard NimbleGen protocol.
|
| |
|
| Channel 2 |
| Source name |
H3.3 DNA nuc
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
age: embryos
strain: N2 (Bristol)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Detailed protocol at http://nettie.fhcrc.org/modencode/protocols/Worm_Protocol.doc
|
| Label |
Cy5
|
| Label protocol |
Standard NimbleGen protocol.
|
| |
|
| |
| Hybridization protocol |
Standard NimbleGen protocol.
|
| Scan protocol |
Standard NimbleGen protocol.
|
| Description |
600mM NaCl-exracted chromatin.
|
| Data processing |
Adjusted log base 2 ratios of Cy3/Cy5 were computed using the method of Peng, et al (BMC Bioinformatics, 2007,8:219,PMID 17592629). The adjusted log ratios were converted to standard deviates by subtracting their mean and dividing by their standard deviation. (NOTE: the supplementary files have the adjusted log ratios, not their standard deviates.)
|
| |
|
| Submission date |
Nov 05, 2009 |
| Last update date |
Apr 11, 2012 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
[email protected]
|
| Phone |
206-667-4850
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Basic Sciences
|
| Lab |
Henikoff
|
| Street address |
1100 Fairview AV N, A1-162
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
| |
|
| Platform ID |
GPL7098 |
| Series (1) |
| GSE18898 |
A native chromatin purification system for epigenomic profiling in C. elegans |
|
