|
| Status |
Public on Jul 26, 2017 |
| Title |
At_root.tip.ATAC_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Root tip
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain/background: Col-0
tissue or cell type: 1 cm root tip
nuclei purification method: INTACT streptavidin affinity purification
|
| Treatment protocol |
One centimeter root tips or fully differentiated root zone (above first fully expanded root hairs but below any lateral roots) were harvested using a razor blade. Total root tip nuclei were purified using INTACT affinity purification or by tissue lysis followed by sucrose sedimentation. Arabidopsis root hair and non-hair cell nuclei were purified by INTACT from the fully differentiated root zones.
|
| Growth protocol |
All plants were grown under 16hr light/8 hr dark cycles on vertically-oriented nutrient agar plates.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tn5 Transposase treatment (using the Illumina Nextera kit) was performed on 50,000 nuclei from each sample, followed by isolation of fragmented genomic DNA using the Qiagen PCR purification kit.
Purified transposase-fragmented DNAs were converted to sequencing libraries through a limited number of PCR cycles using indexed primers, followed by purification of library fragments using SPRI beads.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
U3A
|
| Data processing |
Raw reads were aligned to the appropriate genome using Bowtie2 with default parameters.
Mapped reads were filtered to remove those mapping to organelle genomes, and reads with a mapping quality score of q>2 were retained for further analysis.
Peaks (transposase hypersensitive sites; THSs) were identified using the Findpeaks function of the Homer package, with the parameters "-region" and "-minDist 150". Bed files of the THS regions are included for each dataset.
Genome_build: Arabidopsis thaliana TAIR10, Medicago truncatula Mt4.0, Solanum lycopersicum SL2.4, and Oryza sativa IRGSP 1.0.30
Supplementary_files_format_and_content: .bed files containing ATAC-seq transposase hypersensitive site locations as defined using the findPeaks function of the Homer software package.
|
| |
|
| Submission date |
Jul 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Roger B Deal |
| E-mail(s) |
roger.deal@emory.edu
|
| Phone |
404-727-8087
|
| Organization name |
Emory University
|
| Department |
Biology
|
| Street address |
1510 Clifton Rd NE
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE101482 |
ATAC-seq profiling of open chromatin in the root tips of four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) and two Arabidopsis thaliana cell types (root hair and non-hair epidermal cells) |
|
| Relations |
| BioSample |
SAMN07352885 |
| SRA |
SRX3006635 |
