|
| Status |
Public on Mar 08, 2020 |
| Title |
shock |
| Sample type |
SRA |
| |
|
| Source name |
Fagopyrum tataricum Dingku 1
|
| Organism |
Fagopyrum tataricum |
| Characteristics |
tissue: plants stems and leaves
group: shock
|
| Treatment protocol |
The seedlings were in a growth chamber (12/12h light/dark; light intensity 300 μmol m−2 s−1), the control group was at a constant temperature 16-21 ºC; the momery group with cold acclimation (4ºC 6h repeat 4 times ) then 0 ºC 6h; the shock group without cold acclimation 0 ºC 6h directly.
|
| Growth protocol |
The three leaf age seedlings were cultivated in pots of nutritious soil
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was extracted using QIAamp Fast DNA Tissue Kit (Qiagen, Dusseldorf, Germany) following the manufacturer's procedure
The Accel-NGS Methyl-Seq DNA Library Kit (Swift, MI, USA) was utilized for attaching adapters to single-stranded DNA fragments and library construction.
The fragmented DNA samples by using sonication were subjected to bisulfite conversion. The Accel-NGS Methyl-Seq DNA Library Kit (Swift, MI, USA) was utilized for attaching adapters to single-stranded DNA fragments.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Briefly, as protocol shown below, the Adaptase step is a highly efficient, proprietary reaction that simultaneously performs end repair, tailing of 3’ ends, and ligation of the first truncated adapter complement to 3’ ends.
The Extension step is used to incorporate truncated adapter 1 by a primer extension reaction. The Ligation step is used to add the second truncated adapter to the bottom strand only. The Indexing PCR step increases yield and incorporates full length adapters.
Bead-based SPRI clean-ups are used to remove both oligonucleotides and small fragments, as well as to change enzymatic buffer composition. Finally, we performed the pair-end 2×150bp sequencing on an illumina Hiseq 4000 platform housed in the LC Sciences.
Genome_build: Tartary Buckwheat (Pinku1) Genome
Supplementary_files_format_and_content: Scores represent the peak of riches, WinRAR
|
| |
|
| Submission date |
Oct 07, 2019 |
| Last update date |
Mar 08, 2020 |
| Contact name |
Yuan Song |
| E-mail(s) |
421771569@qq.com
|
| Phone |
86-0931-8912560
|
| Organization name |
Lanzhou university
|
| Street address |
the south of Tianshui road
|
| City |
Lanzhou |
| ZIP/Postal code |
730000 |
| Country |
China |
| |
|
| Platform ID |
GPL24740 |
| Series (2) |
| GSE138497 |
Changes of Gene expression in Tartary Buckwheat (Fagopyrum tataricum) under Frozen stress [BS-Seq] |
| GSE138547 |
Changes of Gene expression in Tartary Buckwheat (Fagopyrum tataricum) under Frozen stress |
|
| Relations |
| BioSample |
SAMN12956706 |
| SRA |
SRX6957507 |
