|
| Status |
Public on Apr 30, 2011 |
| Title |
Nucleosomal DNA_Mnase-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Control liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Native chromatin without cross-linking was released from nuclei by incubation in the buffer containing 0.1 N CaCl2, and then digested with MNase for 15 min (partial digestion) and 30 min (full digestion). Mononucleosomal DNA was collected and pooled from both partial and full digestion of four mouse livers. Mononucleosomal and undigested genomic DNA were purified with the Qiagen PCR purification kit after the digestion with protease K. For DNA sequencing, nucleosomal DNA was further modified following the Illumina sequencing protocol and sequenced with an Illumina Genome Analyzer. For ChIP-Seq, after crosslinking, chromatin was sonicated to reduce the size of DNA to 100~1,000 bp, which was further modified for Illumina sequencing as described above.
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
3WT Nuc Map
|
| Data processing |
We obtained approximately 124 millions reads of 36 nt uniquely aligning to mouse genome (mm8, UCSC genome database). Then, we extended 36 nt reads to 120 bp based on the average size of nucleosomal DNA fragments. Nucleosome positions were defined as genomic regions containing at least four extended reads, based on the average reads at each sequencing locus with 20% FDR. ChIP-Seq binding regions were identified with an input-directed algorithm GLITR.
|
| |
|
| Submission date |
Apr 29, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jonathan Schug |
| E-mail(s) |
jschug@pennmedicine.upenn.edu
|
| Phone |
215 898 0773
|
| Organization name |
University of Pennsylvania
|
| Department |
School of Medicine
|
| Lab |
Next-Generation Sequencing Core
|
| Street address |
12-156 Smilow Ctr Trans Research
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104-5160 |
| Country |
USA |
| |
|
| Platform ID |
GPL9185 |
| Series (1) |
| GSE26729 |
The Nucleosome Map of the Mammalian Liver |
|
| Relations |
| SRA |
SRX059741 |
| BioSample |
SAMN00262617 |
