|
| Status |
Public on Sep 01, 2017 |
| Title |
Arabidopsis thaliana (Col-0, 11 days) |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis thaliana (Col-0, 11 days) _Whole organism
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain: Col-0
treatment: grown for 11 days
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
A. thaliana seeds were surface sterilized with 70% ethanol, then stratified at 4 degrees celsius for 2 days. Seeds were then sown on 1/2 Murashige and Skoog media containing 1% agar, and grown vertically for 11 days under short-day photocycles at 22 degrees celsius (8 hr light/ 16 hr dark) at a density of about 100 seeds per 10cm2 plate. Genomic DNA was prepared as manufacturer’s instruction.
5-10ug of gDNA was sheared to >10kb using g-tube (Covaris). The sheared DNA was treated with DNA damage repair mix followed by end repair and ligation of SMRT hairpin adapters using SMRTbell Template Preparation Reagent Kit (Pacific Biosciences). Fragments without adaptors are digested with exonuclease. Libraries were sequenced on Pacific Biosciences RSII sequencer using standard protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PacBio RS II |
| |
|
| Data processing |
SMRT sequencing reads were processed and mapped to the respective reference genome sequences using the SMRTPortal Analysis platform, v.2.3.0 with BLASR mapping algorithm using the standard mapping protocol and the modifications protocol using default parameters.
Genome_build: TAIR10
The pipeline used to detect the modifications is called “DNA Modification Detection with SMRT Sequencing using R” and can be found at https://github.com/PacificBiosciences/kineticsTools. Interpulse durations (IPDs) were measured for all pulses aligned to each position in the reference sequence. The format of the output CSV/GFF files with modifications is described at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf. The CSV file contains statistical analysis of each position in the reference. The GFF file includes sequence contexts only for sites of putative modification defined as positions with p-values of 0.01 or less.
Supplementary_files_format_and_content: GFF and CSV files
|
| |
|
| Submission date |
May 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Denis Tolkunov |
| Organization name |
DOE Joint Genome Institute
|
| Street address |
2800 Mitchell Dr
|
| City |
Walnut Creek |
| State/province |
CA |
| ZIP/Postal code |
94598 |
| Country |
USA |
| |
|
| Platform ID |
GPL20197 |
| Series (1) |
| GSE68860 |
Genome-wide single-molecule sequencing of 6-methyladenine in eukaryotes |
|
| Relations |
| BioSample |
SAMN03657260 |
| SRA |
SRX1026807 |
