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Sample GSM3473456

Query DataSets for GSM3473456

Status

Public on Mar 31, 2022

Title

m2_3

Sample type

SRA

Source name

seeds

Organism

Fagopyrum tataricum

Characteristics

Stage: green fruit stage
tissue: seeds

Treatment protocol

For the transcriptome sampling, seeds at three developing stages (13, 19, 25 dpa) were collected from the same individual, and seeds with the same developing stage from three plants comprised of three replicates. the collected samples were flash frozen in liquid nitrogen and stored at −80°c until further use.

Growth protocol

Seeds of Tartary buckwheat (MIQIAO 1) were collected in 2016 at the experimental field of College of Life Science, Sichuan Agricultural University (Lat. 29°97’ N, 102°97’ E, Alt. 580 m), China. It had been introduced to the field and grown in the same ecoenvironmental and cultivation conditions for five years. We observed the seed development process from anthesis till maturation in April-May, 2016. Seeds were hand-collected at intervals of two days, from the beginning of seed until full maturity,covering a total range of 30 d.

Extracted molecule

total RNA

Extraction protocol

Buckwheat seeds were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Description

Tartary buckwheat

Data processing

Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Containing adapter, reads Containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, Considering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: http://www.mbkbase.org/Pinku1/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

Submission date

Nov 14, 2018

Last update date

Mar 31, 2022

Contact name

Moyang Liu

E-mail(s)

cooljeep@sjtu.edu.cn

Organization name

Shanghai Jiao Tong University

Department

School of Agriculture and Biology