|
| Status |
Public on Aug 06, 2018 |
| Title |
treeShrew_muscle_MNase-seq |
| Sample type |
SRA |
| |
|
| Source name |
muscle
|
| Organism |
Tupaia belangeri |
| Characteristics |
tissue: muscle
developmental stage: adult
gender: male
genotype: wild type
|
| Treatment protocol |
Tissues were obtained and immediately fixed in 1% V/V formaldehyde at room temperature for 10 min, followed by neutralization with 2.5M glycine (Sigma) and washed with PBS. Then the fixed tissues were homogenized with a T10 homogenizer (IKA) and collected by centrifugation. The collected samples were incubated in hypotonic buffer for 20 min and homogenized for 10-20 strokes.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Pellets were washed with MNase digestion buffer (10mM Tris pH7.4, 15mM NaCl, 10mM KCl, 1.5mM CaCl2), after which were collected by 350g centrifugation for 5 min at 4°C. Pellets were further suspended with digestion buffer containing MNase (NEB, M0247S) and incubated at 37°C, then stopped by 2× stopping buffer (0.6% SDS, 40mM EDTA, 40mM EGTA).
E7370 kit was used for library construction. And the samples were indexed using Illumina Truseq indexes. The cycle number of the amplification was 4 or 5.
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
MNase-seq reads were filtered by inhouse scripts to get high quality reads.
High-quality reads were aligned to the corresponding genome using bwa (v0.7.13-r1126) with default parameters.
The PCR duplicates were removed by samtools (v1.3.1) rmdup command. The uniquely mapped reads with map quality greater than 30 were kept.
Nucleosome occupancy and position were called by DANPOS2 (v2.2.2) with parameters -jd 147 -m 1 --extend 74.
Genome_build: human: hg19, monkey: rheMac2, tree shrew: tupBel1, mouse: mm9, pig: susScr3
Supplementary_files_format_and_content: bigWig files were generated using DANPOS2; scores represented nucleosome occupancy.
|
| |
|
| Submission date |
Nov 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yumei Li |
| E-mail(s) |
yumeil1@uci.edu
|
| Organization name |
University of California, Irvine
|
| Department |
Department of Biological Chemistry
|
| Street address |
825 Health Sciences Road
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL24233 |
| Series (2) |
| GSE106578 |
Nucleosome profiles for mammalian tissues [Mnase-Seq] |
| GSE106580 |
Nucleosome profiles for mammalian tissues |
|
| Relations |
| BioSample |
SAMN07981789 |
| SRA |
SRX3367397 |
