|
| Status |
Public on Nov 03, 2017 |
| Title |
At_mesophyll.cell.ATAC_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Leaves 5 and 6 from 21 day old plants
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
cell type: mesophyll cell
nuclei purification method: INTACT streptavidin affinity purification
ecotype: Col-0
|
| Treatment protocol |
Entire shoot systems were collected from seedlings for purification of stem cell nuclei. Leaves number 5 and 6 were collected for purification of mesophyll cell nuclei. Niclei from each tissue were purified by INTACT.
|
| Growth protocol |
All plants were grown under 16hr light/8 hr dark cycles on 1/2 MS plates for seedling collection (for stem cell) and on soil for leaf tissue collection (for mesophyll cells)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tn5 Transposase treatment (Using the Illumina Nextera kit) was performed on 25,000 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 |
| |
|
| Data processing |
Raw reads were aligned to the Arabidopsis TAIR10 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" "-minDist 150" and "-regionRes 1". Bed files of the THS regions are included for each dataset.
Genome_build: Arabidopsis thaliana TAIR10
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 27, 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) |
| GSE101940 |
ATAC-seq profiling of open chromatin in Arabidopsis thaliana shoot apical meristem stem cells and leaf mesophyll cells. |
|
| Relations |
| BioSample |
SAMN07418708 |
| SRA |
SRX3041702 |
