|
| Status |
Public on Dec 22, 2023 |
| Title |
Day15, Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
pod
|
| Organism |
Psophocarpus tetragonolobus |
| Characteristics |
tissue: pod
genotype: FP15
age: Day 15 after anthesis
|
| Growth protocol |
Each biologilca replicates were collected from different individual plants grown in the growth chamber at 26/20°C temperature with 12-hou adylength throughout
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Rneasy Plant Mini Kit with DNase treatment, according to the manufacturer’s instructions
Library prep was performed with polyA non-stranded library for mRNA-seq and sequenced using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base calling was done by Real-Time Analysis (RTA).
Raw PE reads were trimmed against adaptor sequences by fastp before being map to the genome using HISAT2 v2.0.5 with default settings
Uniquely and correctly mapped reads wre quatitated using featureCounts v1.5.0-p3.
Gene expression level was then normalised by Fragments Per Kilobase Per Million (FPKM).
Assembly: PRJNA808222
|
| |
|
| Submission date |
Oct 30, 2023 |
| Last update date |
Dec 22, 2023 |
| Contact name |
Fei Sang |
| E-mail(s) |
feisang@gmail.com
|
| Organization name |
Nottingham University
|
| Street address |
QMC
|
| City |
Nottingham |
| ZIP/Postal code |
NG8 2UH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL33895 |
| Series (1) |
| GSE246575 |
Transcriptomic profiling of purple winged bean pods |
|
| Relations |
| BioSample |
SAMN38042958 |
| SRA |
SRX22289676 |
