|
| Status |
Public on Jan 30, 2018 |
| Title |
LS3 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
100-day-old roots
|
| Organism |
Ipomoea batatas |
| Characteristics |
tissue: roots
cultivar: 15-94
age: 100-day-old
|
| Growth protocol |
Roots of both cultivars were transferred to pots (one per pot) with 18 replicates each in greenhouse under natural light conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using Trizol (Sigma), and then were treated with TURBO DNA-free kit (ambion) for removing DNA contamination.
Libraries were constructed through using TruSeq Stranded mRNA in accordance with the standard Illumina instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
low starch S3 period replicate1
|
| Data processing |
Clean reads were acquired from initial pair-end reads after trimming low quality (Q < 20) and adaptor sequences by SeqPrep version 1.1
Clean reads from high starch and low starch samples were pooled together to perform the de novo transcriptome assembly using Trinity program (version 2.3.2) with the default K-mer parameter and minimum K-mers coverage of ten, and only transcripts whose length is no less than 200 bp were remained for continue analysis.
Unigenes were annotated by searching against the protein databases including NCBI nr protein database (NCBI non-redundant database), Swiss-Prot database, Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and Cluster of Orthologous Group (COG) database using BLASTX program with the expectation value less than 10-5.
Differentially expressed genes were identified with the edgeR package. Classic model of edgeR was used for the differential expression analysis with false discovery rate (FDR) of 0.05 and two-fold change of Fragments Per Kilobase of gene per Millon mapped reads (FPKM) as significant cutoffs.
Functional enrichment analysis was performed using GOstats. With the hypergeometric test p-value less than 0.001 and gene number more than 50, we got the Gene Ontology enrichment terms. For KEGG enrichment pathways, we used p-value less than 0.01 and gene number more than 5 as threshold.
Supplementary_files_format_and_content: txt file of FPKM value for each sample
|
| |
|
| Submission date |
Jul 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Dong Wang |
| E-mail(s) |
dongwang@ncu.edu.cn
|
| Phone |
(86) 15921240757
|
| Organization name |
Nanchang University
|
| Street address |
Hong Gu Tan New Road, No. 999
|
| City |
Nanchang |
| State/province |
JiangXi |
| ZIP/Postal code |
330031 |
| Country |
China |
| |
|
| Platform ID |
GPL23698 |
| Series (1) |
| GSE101303 |
De novo assembly and transcriptome analysis of two different starch content Ipomoea batatas cultivars |
|
| Relations |
| BioSample |
SAMN07346156 |
| SRA |
SRX2997653 |
