|
| Status |
Public on Nov 30, 2016 |
| Title |
Col-0_50k_seedling_nuclei_FANS-ATAC-seq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Col-0_50k_seedling_nuclei_FANS-ATAC-seq
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype background: Col-0
genotype/variation: wild type
tissue: whole seedlings
age: 7days
|
| Growth protocol |
The Arabidopsis thaliana accession Col-0 and 35S:H2AX-GFP transgenic plants were grown on a vertical plate with ½ LS media and 1% sugar in long day light conditions (16 hours light / 8 hours dark) for 7-8 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated by chopping fresh whole seedlings or roots, density gradient centrifugation and then FANS. Tn5 integration were performed with 50,000 or as less as 500 purified nuclei. Libraries were constructed with 10-13 cycles amplafication of the Tn5 integration products.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
library strategy: FANS-ATAC-seq
maize_B73_overground_part_FANS-ATAC-seq_1million_reads were mapped to maize B73_5a and the others to the TAIR 10
Regulatory regions were called by HOTSPOT and footprints identified by pyDNase
Genome_build: TAIR 10
Supplementary_files_format_and_content: *BED file, the identified regulatory regions
Supplementary_files_format_and_content: *BW file, the genome coverage of each sample, BigWig format
|
| |
|
| Submission date |
Aug 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
schmitz@uga.edu
|
| Organization name |
University of Georgia
|
| Department |
Genetics
|
| Street address |
B416 Davison Life Sciences
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE85203 |
Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes |
|
| Relations |
| BioSample |
SAMN05513123 |
| SRA |
SRX2000799 |
