|
| Status |
Public on Aug 22, 2018 |
| Title |
X4_2 |
| Sample type |
SRA |
| |
|
| Source name |
seeds
|
| Organism |
Fagopyrum tataricum |
| Characteristics |
developmental stage: initial maturity stage
tissue: seeds
cultivar: XIQIAO NO.2
|
| 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 (XIQIAO NO.2) 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 Vonstruction 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 |
X4_2
|
| 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 Vontaining adapter, reads containing poly-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 or raw counts for each Sample. A FASTA file with transcript sequence is included on the series record.
|
| |
|
| Submission date |
Mar 16, 2018 |
| Last update date |
Aug 22, 2018 |
| Contact name |
Moyang Liu |
| E-mail(s) |
cooljeep@sjtu.edu.cn
|
| Organization name |
Shanghai Jiao Tong University
|
| Department |
School of Agriculture and Biology
|
| Street address |
dongchuan road 800
|
| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
| |
|
| Platform ID |
GPL24740 |
| Series (1) |
| GSE111937 |
Next Generation Sequencing Facilitates Quantitative Analysis of seed development of Tartary buckwheat Transcriptomes |
|
| Relations |
| BioSample |
SAMN08723079 |
| SRA |
SRX3803088 |
