|
| Status |
Public on Dec 05, 2011 |
| Title |
Total nuclei DNA 1 (Nuc10_20110313_3) |
| Sample type |
SRA |
| |
|
| Source name |
total nuclei
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
age: adult
strain: JJ2289
tissue: whole organism
sample type: total nuclei
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
INTACT (supplementary file INTACT_ChIP_protocol.rtf)
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
MNase-protected DNA fragments in total nuclei
Illumina HiSeq 2000, Flow cell:v2.5, Software:HCS1.3.8/RTA 1.10.36
average insert size is 139.63
In addition to worm DNA, Total_nuclei_20110313_3 raw files contain pooled fruit fly and yeast DNA from unrelated experiments. Paired
end reads that mapped to multiple organisms have been removed
from the sam and wig supplementary files.
|
| Data processing |
1. We used Novoalign to map paired-end 25bp reads to release W220 of the C. elegans genomic sequence obtained from WormBase. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Total_nuclei_20110313_3.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Total_nuclei_20110313_3.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.
|
| |
|
| Submission date |
Aug 12, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
|
| 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 |
GPL13657 |
| Series (1) |
| GSE31602 |
Tissue-specific nuclei purification from animal models for genome-wide expression and chromatin profiling. |
|
| Relations |
| SRA |
SRX093262 |
| BioSample |
SAMN00714190 |
