|
| Status |
Public on Dec 07, 2017 |
| Title |
193H rep 1 [WGS] |
| Sample type |
SRA |
| |
|
| Source name |
Aerial rosette tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Aerial rosette tissue at 21/22 DAS (days after sowing)
line: epiHybrid 150
|
| Treatment protocol |
Aerial rosette tissue 21/22 days after sowing (DAS) was harvested.
|
| Growth protocol |
Arabidopsis lines (epiRILs 92, 150, 193, 232 and epiHybrids 92H, 150H, 193H, 232H and Col-wt) were grown in a climate-controlled growth chamber in long day (16h light, 8h dark) conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Plant tissues were ground in liquid nitrogen and DNA was extracted using a CTAB-based extraction protocol.
Approximately 5000 ng of total DNA was submitted to the Beijing Genome Institute (BGI) for library construction and sequencing on an Illumina HiSeq4000 instrument.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls performed using Illumina’s real-time analysis software (RTA).
Quality filtering and adapter trimming of BS-seq reads were done using Cutadapt (Q20). Reads with less than 40 bps were discarded.
WGS reads were aligned to the TAIR10 genome assembly using BWA.
SNPs, TE insertions and deletions were identified
Genome_build: TAIR10
Supplementary_files_format_and_content: None
|
| |
|
| Submission date |
May 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Maike Stam |
| Organization name |
University of Amsterdam
|
| Department |
Swammerdam Institute for Life Sciences
|
| Street address |
Science Park 904
|
| City |
Amsterdam |
| ZIP/Postal code |
1098XH |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL21785 |
| Series (2) |
| GSE99481 |
Genome re-sequencing of Arabidopsis epiRILs and epiHybrids |
| GSE99482 |
Arabidopsis epiRILs, epiHybrids and Colombia wild type |
|
| Relations |
| BioSample |
SAMN07179320 |
| SRA |
SRX2871436 |
