|
| Status |
Public on Nov 29, 2021 |
| Title |
TM-1-leaf_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
TM-1-leaf
|
| Organism |
Gossypium hirsutum |
| Characteristics |
tissue: leaf
age: 20 days
|
| Treatment protocol |
none
|
| Growth protocol |
The allotetraploid cotton cultivar Gossypium hirsutum was used in this study. Cotton seeds were soaked in water for 24 h, then transferred to soil in pots to continue to grow in a greenhouse with 60 % humidity at 28/25°C and 16/8-h light/dark cycle. Two and three true leaves were collected from 20-old plants and ground into fine powder using liquid nitrogen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were prepared using Trizol followed by DNase I treatment and removal of majority of mRNAs with oligo(T)-conjugated magnetic beads.
The enriched mRNA was subse- quently used for RNA-seq library preparation following the standard protocol for preparing Illumina RNA-seq libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Raw reads of all sequencing data were trimmed using fastp (Chen et al., 2018b) based on the quality value (Q≥25) and read length (≥20 bp).
The trimmed reads RNA-seq data were mapped to the G. hirsutum reference genome with Hisat2 (Kim et al., 2015a).
Aligned reads with mapping quality (MapQ) less than 30 were removed using samtools (Li et al., 2009).
FPKM computed from StringTie (Pertea et al., 2015) was used to measure the expression level of each gene.
Genome_build: NBI_Gossypium_hirsutum_v1.1
Supplementary_files_format_and_content: FPKM files were generated from StringTie
|
| |
|
| Submission date |
Jan 21, 2021 |
| Last update date |
Nov 29, 2021 |
| Contact name |
Li Wen Zhang |
| E-mail(s) |
wzhang25@njau.edu.cn
|
| Organization name |
Nanjing Agricultural University
|
| Street address |
No.1 Weigang
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL29633 |
| Series (2) |
| GSE165244 |
Profiling of H3K4me3 and H3K27me3 and their roles in regulating gene transcription in allotetraploid cotton (RNA-Seq) |
| GSE165245 |
Profiling of H3K4me3 and H3K27me3 and their roles in regulating gene transcription in allotetraploid cotton |
|
| Relations |
| BioSample |
SAMN17469048 |
| SRA |
SRX9908784 |
