|
| Status |
Public on Feb 12, 2019 |
| Title |
Male 2.5 min digestion SSP |
| Sample type |
SRA |
| |
|
| Source name |
Male F123 mESCs from Cast/129 backgrond
|
| Organism |
Mus musculus |
| Characteristics |
strain background: Cast/129
Sex: Male
cell line: F123
cell type: mES cells
|
| Treatment protocol |
Nuclei are isolated and treated with a limited amount of micrococcal nuclease for a specific amount of time
|
| Growth protocol |
Cells are grown under standard mESC culture conditions (15% FBS, serum + LIF, 1X Pen/Strep) on 0.1% gelatin (following two passages on mitotically inactivated MEF feeders)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells are lysed using a standard phenol-choloroform-isoamyl alcohol purification
Mnase-SSP is performed using the single-stranded library prep of Gansauge and Meyer (Nature Prot. 2013)
Libraries are sequenced with a custom read 1 primer on Illumina MiSeq or NextSeq instruments
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ML_2.5
Male F123 mESCs from Cast/129 backgrond
|
| Data processing |
library strategy: Mnase-SSP
Reads were mapped to a combined Burrows-Wheeler reference of mm10 using bowtie2. They were then filtered using custom Python scripts to generate deduplicated, sorted, indexed BAM files
Genome_build: mm10
Supplementary_files_format_and_content: processed data are aligned, deduplicated, sorted, and indexed BAM files that all scripts in the associated GitHub account
|
| |
|
| Submission date |
Jan 14, 2019 |
| Last update date |
Feb 14, 2019 |
| Contact name |
Vijay Ramani |
| Organization name |
UCSF
|
| Department |
Biochemistry & Biophysics
|
| Lab |
Ramani Lab
|
| Street address |
600 16th St, GH-S312B
|
| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE125053 |
High-resolution analysis of chromatin structure by Mnase-SSP |
|
| Relations |
| BioSample |
SAMN10741255 |
| SRA |
SRX5247945 |
