|
| Status |
Public on Dec 01, 2012 |
| Title |
Col-0 Mnase |
| Sample type |
SRA |
| |
|
| Source name |
2-3 week seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain: Col-0
|
| Growth protocol |
Strains were grown under long day conditions for 2-3 weeks.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mnase digested DNA was size selected from an 2% agarose gel using the QIAEX II gel extraction kit (Qiagen).
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mnase digested DNA
|
| Data processing |
Image analysis and base calling were performed using standard illumina pipelines.
MNase-Seq reads were aligned to the TAIR10 genome via the Bowtie software.
Nucleosomes were called in each strain using the TemplateFilter software.
Nucleosomes in each strain were combined and quantile normalized while the highest 5% by read count were removed to alleviate sequencing bias.
Differential nucleosomes were called using a combination of 2 fold change and poisson score less than .001.
Genome_build: TAIR10
Supplementary_files_format_and_content: peak file with nucleosomes occuring in Col-0 or nrpe1
|
| |
|
| Submission date |
Jun 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
M Jordan Rowley |
| E-mail(s) |
jordan.rowley@unmc.edu, jordrow@gmail.com
|
| Phone |
7343580454
|
| Organization name |
Univ of Nebraska Medical Center
|
| Department |
GCBA
|
| Lab |
Rowley
|
| Street address |
601 S Saddle Creek Rd
|
| City |
Omaha |
| State/province |
NE |
| ZIP/Postal code |
68106 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE38401 |
Nucleosome remodeling by the SWI/SNF complex in non-coding RNA-mediated transcriptional gene silencing (MNase-Seq) |
| GSE38464 |
Nucleosome remodeling by the SWI/SNF complex in non-coding RNA-mediated transcriptional gene silencing |
|
| Relations |
| SRA |
SRX151582 |
| BioSample |
SAMN01036876 |
