|
| Status |
Public on May 14, 2021 |
| Title |
9DPA fiber WT rep2 |
| Sample type |
SRA |
| |
|
| Source name |
9 DPA fiber
|
| Organism |
Gossypium hirsutum |
| Characteristics |
tissue: fiber
genotype/variation: wild type
developmental stage: 9 DPA
|
| Growth protocol |
All plants grown in field
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted from 9 DPA fibers by using RNAprep Pure Polysaccharide Polyphenol Plant Total RNA Extraction Kit (Tiangen, China)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
FastQC software (Fastp V0.20) used for basecalling.
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. At the same time, Q20, Q30 and GC content the clean data were calculated.
Hisat2 was selected as the mapping tool. The number of perfect clean tags for each gene was calculated and then normalized in fragments per kilo bases per million mapped Reads (FPKM) using the described method.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq R package (1.10.1). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Genome_build: TM1
|
| |
|
| Submission date |
May 14, 2021 |
| Last update date |
May 15, 2021 |
| Contact name |
Yang Li |
| E-mail(s) |
liy@mail.ccnu.edu.cn
|
| Organization name |
central china normal university
|
| Department |
School of Life Science
|
| Street address |
NO.152 Luoyu Road
|
| City |
Wuhan |
| ZIP/Postal code |
430079 |
| Country |
China |
| |
|
| Platform ID |
GPL30129 |
| Series (1) |
| GSE174452 |
Transcriptome deep sequencing (RNA-seq) analysis on 9 DPA fibers from wild type and GhWRKY16-RNAi |
|
| Relations |
| BioSample |
SAMN19193840 |
| SRA |
SRX10881866 |
