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Sample GSM4109897 Query DataSets for GSM4109897
Status Public on Mar 08, 2020
Title memory
Sample type SRA
 
Source name Fagopyrum tataricum Dingku 1
Organism Fagopyrum tataricum
Characteristics tissue: plants stems and leaves
group: memory
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 SAMN12956707
SRA SRX6957506

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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